The power of belief

For my most recent campaign, I actually undertook to do this (and then nobody really bothered with any factions cause the game was set in the Inner Planes). It still turned out rather unbalanced, mostly because some of the restrictions and limitations (which I really like having, instead of feats that just provide benefits) are really rather excessive. Somehow I feel that's still okay though, since not all factions should be created equal.

Here's the rather long layout (includes some non-canon groups):

Faction Briefs Their Benefits, Weaknesses, and Restrictions

The Athar are most commonly found around the Great Spire in the Outlands, but members also travel with relative frequency to the Astral Plane. They believe the deities are unworthy of worship, and to do so reinforces their subjugation of mortals. To the Lost, deities are just incredibly powerful individuals, but are just as flawed as lesser beings and should not be idolized.
Benefit: Athar receive a +4 bonus to saves against mind-affecting or otherwise compulsive (ie. quest) divine spells.
Weakness: Members of the Athar cannot willing have any divine spell cast on them by a Cleric who follows a specific god or pantheon (as opposed to a Cleric of a force such as Death or a Druid).
Restrictions: Clerics who follow gods or pantheons cannot join the Athar.

The Bleak Cabal is most commonly found in Pandemonium and its gate-town, Bedlam. It’s members believe the multiverse has no purpose or deeper meaning, and every individual must find their own reasons and motivation from within. Though largely humanist in nature, the Bleakers often fall prey to depression and madness due to the implications of their beliefs. They can often be found supporting soup kitchens and other works of relief across the gate-towns and Sigil.
Benefit: Bleak Cabal members are immune to spells that cause madness and may make a save against the ESP spell even though not normally allowed one.
Weakness: At the beginning of each game day a Bleak Cabal member must roll 1d20. If the result is a 1 the Bleaker won’t do anything that day unless philosophically argued into doing it. Meaning you’ll just stand around and watch other people die.
Restrictions: Lawful characters cannot join the Bleak Cabal

The Doomguard calls the negative Quasielemental Planes its home, though wild rumors place some Sinkers as fortifying in the Abyss as well. Their philosophy revolves around entropy, the force of decay that they believe to be the only constant on the planes. Whether that entropy needs to be assisted or stymied varies from member to member, but they have developed reputation as destruction-mongers.
Benefit: All members of the Doomguard have martial weapon proficiency in all swords and receive a +1 bonus to attack with any sword.
Weakness: Members of the Doomguard are resistant to healing. A Doomguard member must fail a Will save or have the effects of any healing spell cast on them minimized (meaning all die rolls are replaced by 1s)
Restrictions: Clerics who channel positive energy cannot join the Doomguard.

The Dustmen have their outpost upon the Negative Energy Plane, though a number of them are still active in Sigil's mortuary. They believe that this life is a shadow of real existence, and that everyone has already died and transitioned to this poor substitute. Seeing no value in this life, the Dustmen accept death, and work to prepare themselves for True Death and whatever stage of existence exists beyond it.
Benefit: The Dead Truce – Undead will ignore a Dustman provided the Dustman makes no attempt to harm them. This applies only to the Dustman, not his friends, and once the dustman takes action to harm these undead then they treat him normally.
Weakness: Dustman philosophy runs counter to the idea of raising and resurrection, so they are always partially resistant to the idea. A Dustman must fail a saving throw against any spell to bring them back from the dead in order for it to work.
Restrictions: None, anyone can join the Dustmen.

The Fated are often found in Ysgard and its gate-town, Glorium. The Takers accept that life is tough, but assert that it's survival of the fittest, and that each individual has the right to do whatever it takes to survive and prosper. The multiverse exists for those that can take it, and those who won't fight for their piece deserve to be shoved aside. The Fated weren't much loved before the Faction War, and now that their former factol is blamed for beginning the war, many across the planes intensely distrust them.
Benefit: The Fated choose one non-class skill. That skill is always considered a class skill, and they receive a +2 bonus to all checks in that skill.
Weakness: Members of the Fated cannot receive or perform charity, they must pay and be paid (even if the sum is immaterial) for everything.
Restrictions: Lawful good characters cannot join the Fated

The Fraternity of Order is centered on Mechanus and its gate-town, Automata. Understanding the laws of the multiverse provides influence over it, the Guvners say, and those that learn to exploit these rules will have true power. Their hunger for power is well known, and most folks are watchful of them despite their relatively inoffensive nature.
Benefit: Members of the Fraternity of Order may cast Comprehend Languages once per day as a spell-like ability. Knowledge (local) is always a class skill for them and they receive a +2 bonus on all checks with that skill.
Weakness: Members of the Fraternity of Order will not willingly break a law, but may freely break laws if they have a loophole to avoid the penalties.
Restrictions: Only lawful characters may join the Fraternity of Order

The Free League is spread evenly around the Outlands and gate-towns, spreading its philosophy of individual independence from the dictates of others. The Indeps believe the minds of the planes should be free from the thought police of the factions, and allowed to develop their own beliefs. While not advocates of revolution like the Revolutionary League, the Free League has often been persecuted by various groups because of its resistance to authority.
Benefit: +2 bonus on all saves vs. charm and enchantment effects.
Weakness: Indeps cannot appeal to fellow members of their faction for anything.
Restrictions: Anyone can be an Indep

The Harmonium is mainly found in Arcadia and the Upper Planes, enforcing its belief in a unified, planes-wide organization. Peace, the Hardheads say, can only be achieved by getting every person across the planes to believe in the same ideals. Naturally, their beliefs are best suited for the task, so peace requires enlisting everyone into being a member of the Harmonium. While seemingly well meaning, the Hardheads have clearly gotten out of hand on a number of occasions, and people across the planes are often polarized between seeing them as saviors or thugs.
Benefit: Members of the Harmonium may use Charm Monster once per day as a spell-like ability.
Weakness: Harmonium members who disobey the orders of their Faction superiors gain one negative level until they have undergone atonement for it.
Restrictions: Only Lawful characters may join the Harmonium

The Mind's Eye is a neophyte organization, largely spread evenly across the Hinterlands of the Outlands. Also known as Seekers or Visionaries, they see the multiverse as a testing ground, a place designed to help one pursue self-discovery and personal growth. Only through this path can individuals move up the latter of existence. The catch is, they tend to perceive their surroundings as their personal playground, and their self-centered quality rivals that of their forebears, the Sign of One and the Believers of the Source.
Benefit: Members of the Mind’s Eye may use remove fear once per day as a spell-like ability. They may also automatically take 20 on survival checks to determine direction, no matter the circumstances.
Weakness: Members of the Mind’s Eye receive a -2 on Charisma-based skill checks when dealing with people who recognize their faction membership.
Restrictions: One part of the character’s alignment must be ‘neutral’ (ie. neutral good, chaotic neutral) to join the Mind’s Eye

The Revolutionary League is a loosely knit alliance of various anti-authoritarian cells spread across the planes, with its central holdings in Carceri. The Anarchs seek freedom from authority, and the total liberation of the planes from high-ups and hierarchies. Only once the chains of society are cast down will everyone be free to find the truth of the multiverse. Anarchists to a fault, they are rarely trusted. On the other hand, they often find alliances with the oppressed and dispossessed.
Benefit: Members of the Revolutionary League receive a +4 bonus on disguise and bluff checks.
Weakness: Anarchists can never hold any official title or position and must tithe 10% of their earnings to the oppressed.
Restrictions: Lawful characters cannot join the Revolutionary League.

The Ring-Givers are a rapidly growing faction from Ysgard and now based in Sigil. Focused on freeing themselves from debt and reliance, the Bargainers believe that by coveting material possessions and convincing ourselves they are necessary, we become beholden to them. True freedom, they say, can only be found by giving everything up. Likewise, by giving everything you've got to the multiverse, the multiverse will be persuaded to act in kind. Though most folks laugh at the idea of tossing power or riches away, it can't be denied that they often seem to end up on top of many deals.
Benefit: Ring-Givers receive a +2 bonus on charisma-based skill checks with people who are aware of their faction membership.
Weakness: Ring-givers must give away at least 10% of all their earnings (though it can be to anyone they want, though not fellow party members)
Restrictions: Any character may join the Ring-Givers, but must renounce any inherited wealth before doing so.

The Society of Sensation is based out of Arborea, where it demonstrates its philosophy that experience equals power. That doesn't mean simply length or depth of experience (though those are nice), but breadth. The Sensates believe experiencing something is the only way to understand it, and so to understand the multiverse one must expose oneself to as much of its experiences as possible.
Benefit: Sensates received Darkvision to 60 ft and a +1 bonus to fortitude saves.
Weakness: Only when faced with obvious deadly peril can Sensates refuse new experiences; otherwise they cannot refuse the offer of new experiences.
Restrictions: Anyone can join the Sensates

The Sodkillers are based out of Acheron, and believe firmly that violence is the solution to all life's problems. Whatever the trouble, a suitable amount of force properly utilized will resolve the matter. While not exactly popular, they've come to gain a significant amount of respect and power in Sigil because of the obvious effectiveness of their tactics.
Benefit: Cast detect lie once per day as a spell-like ability
Weakness: A Sodkiller who has captured or defeated a criminal cannot let them go until they’ve been suitably punished.
Restrictions: Only Lawful evil and Lawful Neutral characters may join

The Sons of Mercy are a well-meaning group of white knights hailing from Bytopia, traveling across the planes on a mission to demonstrate the best qualities of good. While recognizing the role of laws in protecting the well-being of a community, the Martyrs feel that because law is corruptible, it should not be a hindrance in achieving the greater good. Likewise, they realize evil is counterproductive to peace in the multiverse, but believe that the best way to promote good is by living as an example and helping individuals reform. While noble, a gentle approach isn't always an effective one, and this has earned them a reputation as idealistic fumblers.
Benefit: Cast detect lie once per day as a spell-like ability
Weakness: Sons of Mercy who stand idly by while a known innocent is punished receive one negative level until undergoing atonement.
Restrictions: Only Lawful good and Lawful Neutral characters may join

The Transcendent Order centers in the serene locale of Elysium, seeking to attain unity of mind and thought. Deliberation and hesitation are flaws from the standpoint of their members, and the Ciphers believe that by purifying action into instinct one can discover their role in the multiverse. That role often brings them into the center of conflicts as a mediating force, bringing balance and calm to otherwise unstable situations.
Benefit: Members of the Transcendent Order receive Improved Initiative as a bonus feat.
Weakness: If the player of a Cipher says they’re going to do something, they cannot retroactive change their mind, they also cannot retroactively say ‘that was out of game’ for an offhand comment.
Restrictions: One part of the character’s alignment must be ‘neutral’ (ie. neutral good, chaotic neutral) to join the Transcendent Order

The Xaositects are everywhere, but find their natural home is Limbo. Chaotic in the extreme, they think that disorder is the true state of the multiverse, and the only state worth seeking. True freedom and strength can only be found by loosing the shackles of reason and conformity according to their example, if not precisely their teachings. Most people simply think them mad, and often the Xaositects only back that up with their bizarre actions and schemes.
Benefit: Xaositects can use babble (the reverse of tongues) once per week as a spell like ability.
Weakness: Xaositects cannot undertake long-term projects such as founding a business, organization, or constructing a building.
Restrictions: Only chaotic characters may become Xaositects.

Sects
Most sects such as the Ragers, Incantifers, and Prolongers are highly exclusive and very, very difficult to get into, making them unavailable for player characters. However, a small number of sects are available to PCs, especially those hailing from the Inner Planes.

Etherfarers are found on the ethereal plane and among its many demiplanes. They believe that everything in the multiverse is mirrored somewhere in the Ethereal, so that by exploring the Ethereal they can come to understand everything. They are very exploratory in nature and friendly to planewalkers, but don’t really stand for anything beyond that.
Benefit: Etherfarers receive a +4 bonus on survival checks while on the Ethereal plane.
Weakness: Etherfarers take a -4 penalty on survival checks off the ethereal plane.
Restrictions: Anyone who has been to the Ethereal can become an Etherfarer.

The Verdant Guild is centered on the Beastlands, but can be found anywhere wilderness is strong. They believe wilderness is essential and must be preserved from the onslaught of civilization, for even civilization cannot exist without wilderness. Wilders work to serve and safeguard wild places in a balanced fashion.
Benefit: Verdant guild members can speak with animals once per day as a spell-like ability and receive a +2 bonus on Knowledge (nature) checks.
Weakness: Verdant Guild members may not take points in ‘civilized’ skills, such as any industrial Craft or city-derived Profession
Restrictions: Only non-evil, non-lawful characters may join.

Mathematicians are centered on Mechanus and hardly ever leave. They believe logic, numbers, and equations govern the multiverse and that these can be derived and solved. This work involves understanding and comprehending mehcanus and makes them very secluded and secretive, for they covetously hold onto their findings.
Benefit: Mathematicians can navigate Mechanus’ Labyrinthine Portal on a successful DC 15 knowledge (the planes) check.
Weakness: Mathematicians may not share any information about Mechanus with non-members.
Restrictions: Only Lawful characters with an intelligence of at least 17 can join the Mathematicians.
The Order of the Planes Militant believes in truth, justice, and righteousness and all that other good upper planar stuff. Based out of Mt. Celestia they are tireless foes of evil who never rest in their task. They range throughout the multiverse trying to right wrongs and spread the general good.
Benefit: Members may use Smite Evil once per day as a spell-like ability.
Weakness: Members suffer a -2 on all charisma based skill checks when dealing with evil beings.
Restrictions: Chaotic members may not join the order, and non-lawful good members who join represent a commitment to attain that mindset in time.

Anatomists are a young sect based primarily on the Inner Planes, though they get around because living things can be found everywhere. Life is the heart of the multiverse and by understanding life, including by cutting it open to see the gooey innards, you can understand the whole multiverse. Academic and kind of creepy, Anatomists are usually singularly focused on the pursuit of knowledge of all kinds of things.
Benefit: Anatomists receive a +2 bonus on any knowledge regarding a life form (including undead and constructs).
Weakness: Only when faced with obvious deadly peril can Anatomists resist learning about new creatures. Otherwise they’re all ears.
Restrictions: A character must have ranks in a knowledge skill governing some type of creature in order to join the anatomists.

The Order of Broken Chains believes that slavery is the root of all evil and only when bondage is ended can the multiverse make any progress. They work tirelessly throughout the multiverse, but especially on the Inner Planes, to free slaves. Abolitionists generally have good intentions, but may be somewhat sort-sighted, as they don’t go in much for dealing with the stuff that comes after throwing off bondage, being too busy hunting down the next slaver.
Benefits: Abolitionists can use true strike once per day as a spell-like ability but only against a slaver.
Weakness: Abolitionists who willfully ignore a case of slavery (not the same as not taking an action because they lack the resources at the moment) receive one negative level until undergoing atonement.
Restriction: Lawful evil characters cannot join.

Cremators are based in the Elemental Plane of Fire and its bordering planes. They have a razor-sharp focus: the multiverse must burn! Pyros are obsessed with fire, flames, and making everything go through a process they believe is essential to the status of reality. Many devolve into simple Pyromania, and look at them as the dangers they are.
Benefit: Pyros cast fire spells and effects at a +1 caster level.
Weakness: When presented with an option to burn something without any consequences, a Pyro must do it.
Restrictions: Lawful Good characters cannot join the Cremators

The Cinderformed believe that fire is a great force of change, and that one must be burned in order to achieve transcendence. However they also believe that burning is destructive and that part must be avoided to achieve transcendence, so they strive to be burned but not burned at the same time. Cremators are based in the Paraelemental Plane of Smoke, but wander throughout the Inner Planes. They are well-liked by most, but feud brutally with the Cremators.
Benefit: Cinderformed receive fire resistance 5.
Weakness: Members of the Cinderformed have a -1 to their will saves
Restrictions: Anyone can join the Cinderformed

The Refracted Association of Tones is based on the Quasielemental plane of Mineral. They are interested in the understanding of sound and how it travels through objects, believing all things are united by patterns of sound. The Crystallites are very eccentric and mysterious, and decidedly a niche group.
Benefit: Crystallites can move with a burrow speed of 5, but only on the Quasielemental Plane of Mineral.
Weakness: Crystallites receive one extra point of damage per die from sonic attacks.
Restriction: Anyone who has been to the Quasielemental Plane of Mineral can join.

Affiliations from PHBII/Complete Champion would work better than bloodlines. Actually, I'd use the setup that they use in Complete Champion that combines affiliations with organizations. First meet the requirements for the Organization to gain the Namer abilities, then improve your affiliation score to go through the ranks. Let rank be a pre-req for faction specific feats, and both be pre-reqs for PrCs.

(sorry for my english, ok? Im brazilian)

I think Faction Powers, or Belief Powers if you prefer, should not be like some power that you activate. It should be something thats always on.

If enough people believes the earth is a flat disc, it just is. One does not need to throw a spell or activate a power for turning it flat... because it just is. And if, at the same time, enough people thinks its a sphere, it just is, too.

SOOO, a chaositec believer should be protected by chance, opportunity, chaos, randomness, all the time. If he is thrown off a building, theres a big chance there wil be a wagon full of sand passing below just the right time (what a luck! ).

If a Godsman' pet died one year ago, he may just have seen a little boy by the street and recognized it as his pet, in a new and evolved form! (Thats great, my pet actually ascended! )

And so on...

Belief should not be a spell-like power that you turns on or off. Or you believe, or you dont. And if you DO believe, you should not be conscious of your belief shaping reality in this or that moment... reality already IS what you believe it to be, since the first day you started believing.

The affiliation system is a good compromise.

Athar Affiliation
Score Title: Benefits and Duties
3 or lower No affiliation.
4 – 10 Namer: You can seek shelter within the Shattered Temple, and can find work there being paid 1d4 gp per week writing pamphlets. You must do menial labor for the Athaon and higher-ups, and if you have a house you must allow higher members of the Faction to stay there at no charge. No priest of a deity can knowingly cast a beneficial spell upon you.
11 – 15 Athaon Fourth: The character gains a +2 sacred bonus to all saves vs. divine magic. You can kip up with a namer, not having to expend money on maintaining a lifestyle. Divine entities of the Powers who recognize you (Knowledge check of appropriate type DC 30 minus ½ CL) receive a +1 morale bonus to attack and damage when fighting you.
16 - 22 Athaon Third: The character is immune to all divine detection magic. Priests of a deity who recognize you or your Athar affiliations receive a +1 morale bonus to attack and damage rolls when fighting you.
22 - 29 Athaon Second: The character is immune to all divine mind-affecting and enchantment effects. The bonuses in combat against you made by divine beings and priests increases to +2, and is automatic (they don’t have to know you’re an Athar beforehand, they instinctively know.)
30+ Athaon First: +6 bonus on Intimidate checks when dealing with agents of the divine. (Whether it be outsiders or priests.) You can borrow any item worth up to 50,000 gp from the faction’s vaults for 1 week. Cannot step foot within the temple of a deity, or face an effect similar to a bestow curse (automatic, without save.) Possibly even call down the wrath of a deity if the temple lies outside of Sigil.

I agree with you.

Trascendent Order Affiliation

3 or lower No affiliation or membership without bonuses.
4 – 10 Namer: All factioneers try to act as fast as possible. For this reason, they gain a +2 bonus to their Initiative bonus. However, a Cipher must act when he is given the opportunity to act – he cannot use the Delay action in combat.
11 - 20 Master of the Heart: A Master of the Heart has learned how to enter a Cipher Trance. The Trance grants him an additional +2 bonus to his Initiative, and a +2 bonus to all attacks and damage made in the first round of combat, as well as to saves vs. mindaffecting effects.
21 - 30 Master of the Mind: The bonuses from the Cipher Trance increase to +4 at this level of involvement.
31+ Master of the Spirit: The Cipher has trained himself to work so hard and so quickly that at this point he is treated as if constantly under the effects of a haste spell. This ability is extraordinary, and cannot be dispelled.

Well, the Planewalker Handbook explicitly says that power comes from belief, not affiliation.

Anyway, Nerfi Ref, considering your argument...

The later do not negates the former. See? Both are valid.