I think that guessing at how KH3 might work absolutely needs to start with guessing at the purposes of the Disney worlds in the game to follow.
The goals we're seeing for KH3's protagonists seem to be as follows:
-Retrieve Master Aqua from the World of Darkness (a likely Riku joint)
-With Aqua in tow, proceed to Castle Oblivion, restore it to the Land of Departure, and give Ventus's heart-fragment back to him from Sora (which requires, at the very least, Aqua and Sora)
This would presumably get us up to the requisite seven Keyblade wielders (Aqua, Ventus, Sora, Riku, Kairi, Mickey, Lea).
Following this, I presume there'd be a push to free Terranort from MX's control over his body, but that doesn't *necessarily* have to happen until the endgame.
None of this, however, creates a justification for the necessary inclusion of Disney worlds in the game. Organization XIII's have-Sora-kill-lots-of-Heartless plot from KH2 doesn't really work anymore, and nor does anything about locking the hearts of worlds.
Master Xehanort mentioned in KH
DD that if the seven keyblade wielders refuse to face him, he'll just go after the Princesses of Heart instead. THAT'S a reason for Disney worlds to be included. I could see this being a plot element that crops up in KH3, but given that there are a bunch of properties Disney/Squeenix will want to include that don't necessarily include princesses (let alone the ones who have been described as Princesses of Heart), I don't think it's sufficient to justify everything that'll be happening in the game.
I'm honestly not sure what'll justify the Disney worlds being a part of the game, so it might end up being a new story element (some sort of new macguffin that Sora needs to collect, perhaps).
However, here's a way I think the game could control pacing fairly well while still having a number of playable stories: something like the chapter system from some of the Suikoden games, or like we saw in Resident Evil 6.
Think of it this way: the game starts off with a tutorial chapter in which you play as Kairi (this is basically a guarantee, I think).
Following this, you can choose to play Riku Chapter 1 or Sora Chapter 1. (Let's just assume that it'll start off with Sora/Donald/Goofy and Riku/Kairi/Lea, with Mickey playing a playable-if-you-die-in-certain-boss-battles role similar to what he had in KH2).
Then assume that there are certain chapter requirements that must be completed in order to unlock subsequent ones (to be sure that all parts of the story keep pace with the others). But you could play through the chapters like Sora/Riku/Sora/Riku/Sora/Riku or Sora/Sora/Sora/Riku/Riku/Riku.
I think there are certain things that this approach would require, one of them being a way to share certain upgrades among your entire party (Bonus Level could handle this pretty well, I think, as could something akin to Birth By Sleep's pleasantly simple passive-ability system).
It would also require some interesting changes in the climactic endgame chapter (for example, how do you handle the sheer number of protagonists that need to be there for the climax?) but I feel like it would end up being a better-paced cross between Birth By Sleep and Dream Drop Distance that would never allow the story to go off the rails.