Toonboom might be the future for a fair bit of animations both new and old, but I don't see it being anytime soon, and possibly not at all for MLP, at least not this generation.
Maybe it's just me but something felt really off about the new animation style in the movie as well. Not to say that it was really bad or anything, I think I've just grown so accustomed to watching the flash animation continuously improve so seeing something so different wasn't really expected.
I personally prefer good old flash for it's consistency and I feel they'll stay with what's worked for them so far. "If it ain't broke, don't fix it" basically