Couple of thoughts on this. Partially rambling. Feel free to ramble along with.
If you've got a Sigil as a City of Doors, and you've got an Outlands with a bunch of gate-towns with portals leading to various afterlife-planes populated by gods, their favored dead, and their servants, then you have a big chunk of Planescape right there, in my opinion. Now, alignment appears to have bitten it in 4e, so arranging 16 planes in a neat circle may have to bite it as well. It doesn't have to -- whatever genius loci governs the Outlands may have a fetish for categorizing and dividing the various planes, demanding that various godly Domains stand in logical relation to one another. But this does lead to a couple of possibilities that we might be able to take advantage of.
1.) The Great Wheel stays the same. The Outlands, a plane of balance and opposites, arranges itself so that gates to planes of allied gods cluster closely together, and gates to planes of gods likely to come into conflict are kept as far apart as metaphysically feasible. This winds up with something much like the Great Wheel.
1a.) But it doesn't have to be exact! For example, it might be more of an Egg: the gates to Upper Planes would naturally cluster more closely together, and those to Lower Planes would repel each other almost as much as they repelled those to Upper Planes, leading to a wider spread. Roads and trade would be easier to maintain for Upper Planes, and in case of attack those gods could support each other more easily, while wider spacing between the Lower Planes makes it inconvenient to troop Blood War armies across the Outlands.
2.) We could rewrite it entirely. Perhaps the gate to Pandemonium must be found high in the jet stream, the tiny gate-town a crazy-quilt collection of flying carpets, floating rocks, and hot-air balloons chasing it around (and sometimes being outpaced by the gate, and having to dash after it). The gate to Limbo appears anywhere someone wants it to if they build an appropriate key, though you never know when and just have to wait and be ready for the opportunity. (Although maybe Limbo has been replaced entirely.) Farthest from the Spire is Faunel, which moves further out every time some idiot tries to pave a road to it. The gate to Mechanus never seems to change its position or distance from the Spire, and so Automata is taken as the "Prime Meridian" of the plane. Etc.
2a.) And what do we do with "unaligned" anyway? Guess they show up at an appropriate god's Domain, or suitably comfortable plane.
3.) Maybe they shift around on occasion. For playability's sake, the Outlands needs to have some sort of predictable trade and travel routes, so that adventures can be planned there, but having a few different logics that shift at regular intervals makes a bit more of a balance between law and chaos. Perhaps every few months you have a short interval where Curst finds itself surrounded at three equidistant points by Excelsior, Automata, and Fortitude, while the citizens of Rigus and Glorium look forward to the rush of profits from arms sales during the days when those two towns are within a day's march of each other.
Something I suggested in another thread is giving the Outlands 30 rings rather than nine, and having them affect all class abilities equally rather than penalizing magical or divine spellcasters disproportionately.