That's all control, though. What does the Vita have that the 3DS doesn't? A second analog stick? Well that's being remedied. Better graphics? Yes. But does that hinder the gameplay? No. Not one bit. Saying you'd prefer the next KH game to be on the Vita rather than the 3DS can't really apply to gameplay. They're capable of delivering the same thing, the only difference is perhaps using their different touch and/or dual-screen mechanics, but then again, that's not "higher tech," now is it? Just different tech.
I think you're underselling the difference between the alternate touch screen technologies chosen by Nintendo and Sony.
Nintendo chose to create a two-screen console, with only the secondary (smaller, non-3D) screen being touch-capable. This means that touch mechanics must be either decoupled from the action, or applied to a temporary copy of the action on the lower screen rather than the main screen (this is why Reality Shift works by having Sora dive into the bottom screen). To complicate this further, the touch screen only understands one touch at a time, which limits its uses somewhat.
Sony chose to give Vita only one screen, but that single main screen is touch-enabled, so touching objects on the screen is more immediate. The screen is multi-touch enabled as well, which offers possibilities of interaction that don't exist on the 3DS (like targeting multiple areas at the same time with special attacks), and there's a second multi-touch screen on the back that can add even more functionality. The additional gameplay possibilities might not be as obvious as, say, those of a second analog stick, but they're certainly there -- imagine using simple gestures on the back to command your allies without taking your hands off the main controls, or having an always-on option to immediately target far-off enemies (like, say, those irksome Mandrakes in Birth by Sleep) by tapping them on the front screen.
And that's not even getting into the fact that differences in processing power need not only be used to improve the looks of what would have been on the screen anyway. Moving up to a more-advanced system could also allow to put more stuff on the screen overall -- more NPCs, more allies, more enemies, more props to interact with, more-connected worlds.
And I'll say it again, just like everyone else has, story is story. Technological limitations have absolutely no bearing on it. How it is presented, yes, but that's not how the story is told, per se.
I can understand where you're coming from in terms of gameplay (I don't agree, but I see where you're coming from), but story? No. I see no reason why you think what you're saying makes sense, I'm sorry.
The thing is, story-as-story is always filtered through the way it's presented, and that can have a rather enormous effect on how that story is perceived. Broken suspension of disbelief, for example, can make a story seem far worse even if it was broken by a failure of presentation rather than a failure of the story on its own terms. As technology can easily allow for fuller suspension of disbelief, it stands to reason that it's not that improbably for one to feel that the story is better for its ability to avoid blatantly low-tech effects.
