Two things.
One, it was trying too hard to do far too much at once. It changed everything from the ground up with only one game before it as a frame of reference. To its defence a LOT of games in the late 80s were experimental sequels, such as Zelda II, the infamous reskin of Doki-Doki Panic as SMB2 and so on, but those were all still good games in their own right. Not that I don't like FF2; I actually quite enjoyed each attempt I've made to play through it (on what must be like my fourth run through the game now, and what I'm confident will be my second time actually beating it... damn it's hard!) but once you happily embrace all the stuff that's completely different to the first with how you develop characters I find it genuinely enjoyable.
Two, it gets a bit repetitive. Every boss fight I've done so far has been a case of having Maria cast Berserk on Guy, having Guy hit it with an Ancient Sword to inflict Curse, then having Guy switch to a better sword to finish it off. Almost every boss fight has been two rounds. Then there's the random encounters: I'm basically spamming Mini and Toad for almost all of them now that they're at a high-enough level to hit almost every time.
As I say, I still like this game, but now that I've played it a lot what I consider to be its real flaws are just getting that much more obvious.
What did you think was ultimately wrong with this game?