I'm going to divide these into two categories. The small and the big.
The small:
*'Trance' is such a bull
. You get it maybe six or seven times throughout the whole game for your most used characters, if you're lucky. It almost invariably happens when you're fighting in a field battle, and its requirements are stupid. When does a boss opponent ever damage you enough to make Trance likely? It's pure chance. It is also not helped by the constant break-up of characters into different plot strands... but I'll be coming to that later.
*The smurfing unending monotony of battle music. There are two types of battle music in the game. Normal battle music and boss battle music. So far, the only breaks in this trend have been when you fight Beatrix in Burmecia and when Zidane is having his pissy little strop in Pandemonium. For God's sake. How hard can it be to add maybe four or five different musical themes for a sequence that happens literally hundreds of times during the course of the game? And the theme doesn't necessarily even have to be different. How about a remix or change of instruments or something?
*The useless and uninteresting Eidelons. They feel tacked on. Whereas FF8 made them a big part of gameplay, in FF9 they revert back to FF7 mode and become what is, essentially, an uninteresting and overly magic spell.
*Redundant characters. Quina doesn't work because he doesn't have a back-story. He also doesn't work because he isn't smurfing funny. There is no wit to him. Constrastingly, Freya has an excellent back-story, but it is explored for all of five seconds. She barely says a word for the rest of the game after Cleyra. Both needn't have been playable characters (why not Beatrix instead?). Freya would have worked as a temporarily playable character. Quina can just die, as far as I'm concerned.
*Lack of FMV sequences. The FMV sequences in FF9 are really quite special at times, but they only seem to be used for major events (the destruction of Burmecia and Cleyra, Brahne's death, Kuja laying waste to Terra). The in-game graphics can be annoyingly vague at the best of times. I don't think I even know what Amarant's face looks like.
The Big:
*Lack of real interest in environments in the final half of the game. The first half of FF9 is absolutely stunning. So many different towns and cities, so many different races and cultures. But once you venture into the forgotten continents, the wonder and fantasy goes rapidly downhill. The Black Mages live in... er... a forest. Eiko lives with moogles (ANNOYING
ES) in a canyon made of rock and nothing else. Oelivert and the Desert Palace were just tedious. Boring, boring, boring. Conde Petie was neat, but nothing we haven't seen before. Terra, again, looked stunning but ultimately had nothing to it and was destroyed before the characters ever really had a chance to explore it. The whole final half was a letdown, and even while Memoria was interesting-looking, it felt too much like the castle you had to explore before you fought Ultimecia in FF8.
*CONSTANTLY BREAKING UP THE CHARACTERS UNNECESSARILY. I cannot stress enough how big a problem this was for me. Constantly your characters are broken up, characters you've invested time into, developing a bond with - growing, eventually, to love, and then they're broken up - often not be seen for f**king hours. This is especially annoying when Garnet and Steiner break from the group in Lindblum before you head off to Gizamaluke's Grotto. Zidane isn't re-united with either until the end of the second disc!
*Developing characters' personalities, and then just giving up. Steiner is a great example of this. Oafish and clumsy, but equally valiant and proud. His introspective moments are among the best instances of dialogue in the whole game, equally so are his early arguments with Zidane. Then, after defeating the monsters Kuja has sent to destroy Alexandria, you barely hear an original word from him for the rest of the game. He simply doesn't say anything of note after that. All you get is generic dialogue that could have been said by ANYONE. Similarly with Freya - exposition and then sod-all for the rest of the game. Instead we are treated to excruciatingly tedious, contrived and cliched soundbites from Amarant, who has a hard time figuring out why he's so fecking stroppy all the time.
*An overly simplistic and boring weapon/armour/ability system. The characters' abilities are barely customisable, and the abilities and weapons are largely dull anyway. There isn't a single interesting Trance move, Eidelon animation or magic spell in the entire game. It's distinctly Pokemon-esque. In fact, I reckon eight-year-olds who play Pokemon would probably find the equip system too easy to use.