The problem with KHII for me (aside from the gratuitous use of Reaction Commands) isn't so much the battle system as it is that there isn't anything in the non Final Mix releases of the game that forces you to actually learn some of the combat's intricacies. Sephiroth is damn near the only boss in vanilla KHII that punishes button mashing, and even then he's still a joke if you use Counterguard and/or Reflect.
Admittedly, it's pretty stupid that it took an entire re-release of the game for them to get it right, and even then, you have to play on Critical Mode to get the most out of it, but a Critical Mode run in KHIIFM really lets the battle system shine. With a lot of the enemy encounters, you actually have to plan out and prioritize how and when you'll use all the tools available to you, which is how the game should have been in the first place.
KHII is a result of them listening to a (part) of their fanbase who thought
1) the sometimes complex level designs weren't fun (-> in II they streamlined worlds)
2) the game could be difficult if you didn't grind (-> II is easier)
and they kinda went to the extreme end of "fixing" these problems. Then II came out and they realized, hey, not all of our fans are children or shitty players, so ever since then they've included a bit more choice in the challenge department and not had such straightforward level design. Of course not all of the things they listened to fans on & thus changed were bad
-inaccurate jumping in the first game -> made it a bit better to control in II
-somewhat clumsy controls overall -> tightened it up
-no camera control on the right analog stick -> camera control with the right analog stick
-swimming world in I -> no (proper) swimming world in II
-gummy ship portions were boring -> gummy ship portions were a bit more exciting
They really do listen to the fans a lot with these games. That's why when BBS got such a great reception they've been taking that kind of gameplay further. If they continue this way, I'd wager that, say, the flow motion stuff will return in III but it'll be changed a bit, perhaps better balanced or a bit more limited to make using all that stuff a bit more strategic. And if the Pokemons ever return, I doubt rubbing them will be in (I guess you might still be able to do it, but it'll probably not be important at all).