Now that there isn't the weight of Xehanort, the Keyblade war, and a dozen disparate character arcs that need to be solved, I don't think any of you need to worry about Verum Rex/Versus XIII/Classic KH Disney stuff taking up too much time. There's room for both if you ask me.
You can contain Sora in Quadratum for a meaty portion of the game, maybe only letting him escape temporarily through some obscure means that let him be with Donald and Goofy before getting zapped back for more Quadratum stuff after clearing a world.