I think that's unfair, for a game like VIII to be hated, while something that's full of holes, and is even "more" cliche than IX, in VII gets applauded for being the best game of all time in some circles.
I'm all for nostalgia, but once it blinds you to the point you can't see inherent flaws, it goes overboard.
My main problem with IX's story is that I was able to more or less guess something, and then instantly have it be true a few minutes later, with no prior knowledge of the game. If I can see something coming, it feels boring. And I'll be honest, I got up to the Final Dungeon, but then quit playing. It wasn't that I chose to quit. Just other things came out. And I felt more inclined to play something I enjoyed. I don't know if the Zidane/Kuja thing ever worked itself out, but the game never did a good job of making me feel like it mattered if it did or not. Based on what other people have told me, there was maybe a half hour of gameplay remaining, and I can get all that's relevant out of the post big bad cutscene. I still have the save file, I just don't feel compelled to go back to it.
When I don't feel compelled to finish a game, I don't know, it just feels like that game failed in its job of hooking me. For a game that is talked about in rarified air (I've had people try comparing it to VI), it felt shallow and half hearted. I didn't feel the same things about the game, and that's fine.
I love the Final Fantasy series. I really do. I have actually played through nearly all of the games in the series. The exceptions being the MMOs, Lightning Returns (which I'm working on), and IX. Each game has its faults, and the series is far from perfect. I'll just never understand the love affair for VII, or IX, or the hatred for VIII and X (some people hate it for whatever reason).