My problem with Square Enix over VII is that in the movie Advent Children, Cloud regresses into this messed up hero instead of the like-able one we last saw in the ending of the game. And they never really explained how he suddenly became Sephiroth-like powerful. I actually liked it, but it was never explained how he became like that. Other than that, I want to remember VII for the game than the movie or the other spin-off games it spawned (although I did like Cloud's costume in AC).
IX is probably the last time the franchise returned to its roots. Just a simple, magical story that isn't too complicated and wasn't trying to be too cool. It was the last FF in PS1 and a bit underrated too. But the story is really enjoyable. I haven't had anything to complain about it. All FFs from X straight to FF-XIII 2 I have issues with one thing or another. But IX is a simple, enjoyable, if a bit underrated experience.