In 3rd Edition, many odd decisions have been chosen, for example, Toril now has the "Great Tree" Cosmology, and various other Campaign Settings, like Eberron, also have their own cosmologies. Many(And I was once one of em..) believe the Multiverse is gone. The various Campaign settings are no longer linked. But hold on for a second...
This can all be reconcilied very easyly. The 3rd edition Toril is NOT the same Toril of 2nd edition, because that Toril was part of the 2nd Edition Multiverse. The same is true of 2nd Edition Krynn.
Awile back there was a science fiction series called Sliders. In this series, the four cast members traveled to alternate Earths, which had a different history, and sometimes different laws of physics. Sometimes these worlds were VERY similiar to our own earth, with just a few minor differences that it would be hard to recognize them at first. For example, in one episode, they thought they had finally arrived home, but realeased it wasn't home when they saw the Goldengate Bridge was Blue.....
In some worlds, they even ran into duplacates of themselves.
This could be applyed to Planescape as well. The Multiverse we know and love from 2nd edition is only one Macroplane if you will. There exist an INFINITE amount of other Macroplanes, beyond the Far Realm, which separates each Existance.
In the Planescape Multiverse we are familiar with, BELIEF is the one defining factor. Other Macroplanes could have their own, different defining factor, such as LOGIC. For example, the old Alternity game's Stardrive setting could be in such an alternate Macroplane.
3rd Edition didn't get rid of the Multverse, it just made it a HELL of a lot bigger....
In fact, this would explain alot of 2nd edition Planescape adnormalities, such as the Keepers and the Chasium. According to the 2nd and 3rd Planescape Monstrious Compendium, The first supposibly came from another Multiverse, and nobody knows where the Chosium comes from, although one man claims it came from a unknown plane which connected to somewhere else
This restores the sense of mystery that was missing in Planescape after all the Planes were reveiled. This is what one of the authors of the "Beyond Countless Doorways" book was talking about.
An interesting hook would be that most of the alternate Multiverses/Cosmologies have a Sigil counterpart, and of coarse, a Lady of Pain....hehe
Basically, the Planes just got a whole lot bigger....hehe
No longer is it "Oh Toril, that backwater Prime world..." now its "Which Toril?(looks over shoulder in fear).
You also can introduce an element of the paranormal into Planescape. Perhaps beings never before seen have begun appearing here and there on the Planes, and some high-ups accross reality have begun to disappear, including high up Celestials and Fiends(even Loths). Sometime later, then return, with no memory of where they've been. Some have vague recollections however, and they remember a reality they can't even begin to describe, a reality that makes the Far Realm look like a pastorial mundane farming village on the Prime by comparison.
:
The key to all the doors...
An intresting concept, it alows for a diversity unheard of even in planescape. This allows DMs a back door to converting their ideas to planescape. Doesn't fit the multiverse? Screw it, its a new macroplane.
Oh, and by the way... Go sliders, woot.
Unfortunetly, this idea could lead to a chaos unheard of, even unto the deepest depths of the Abyss or pandemonium. Creatures whose very existance is a corruption of the planes could conceivably enter the multiverse.
But what would happen if a creature from another reality entered Limbo, and choas shaped it into a growing duplicate of its own reality. Think about it, it would became enough like the other reality that it slides over, its portals to the multiverse still intact... WHAM! The Multiverse is flooded witt creatures that even the Lady of Pain would have cause to fear.
While I think it a cool and creative concept, with it in place, all the rules dissapear.