Many reasons.
The story is a huge and convoluted mess. It tries to accomplish far too much. At first you're introduced to Roxas and his story, which is fine and dandy, except the three hour prologue becomes completely tedious. What's more, after all the hype surrounding his character, you only got to use him for three hours, and then he disappeared until the very end of the game. But that's not all.
The Organization is made out to be an enormous threat in the game, and yet they're barely seen. You don't get a good idea of their motives or personality in the same way that you did in CoM. No, instead, there's Pete and Maleficent.
While Pete is an alright character, I felt that his role was unnecessary. Rather than have him dawdle around, the Organization could have simply manipulated the Disney villains and others more prominently throughout the game. And Maleficent? Her role was so watered down. Gone was the delightfully manipulative and cunning villain; she barely appeared in the first place, but if they had to bring her back, they should have done so with a lot more dignity, IMO.
The Disney worlds are just movie retreads, for the most part. With a few exceptions, such as Space Paranoids, they're essentially the movie in a nutshell with KH characters inserted into them. Whereas KH1 and, later, BBS, often have elements from the films, the plots of their world adaptations still were integral to the plot, especially in the case of the first game. In KH1 the Disney villains all worked together to accomplish a single goal. In KH2 they had absolutely nothing to do with each other, which made the story seem far more disjointed.
Characterization was generally flat, too. Sora didn't really grow or develop like he did in the first game. The only thing that changed was that he became incredibly angry at times. Otherwise he was infinitely more flat than the first game. Likewise, Riku's character suffered in my mind, though at least in his case there was some development, albeit barely anything shown during the game.
I do like Kairi in KH2 because she had a bit more backbone, and some characters such as the Twilight Town gang were fun, but a few gems won't make up for the rest of it.
Granted, the game did get better storywise once Hollow Bastion was revisited, but was it really necessary to revisit every single world? If they were going to do world retreads, they could have done so in a way that was.. more meaningful, I guess. When the Org showed up in these worlds they were there for a split second and gone, or so it seemed.
Big problem with KH2: CoM was barely referred to at all. I know Sora forgot, and that's fine, but Riku remembered, and the "Thank Naminé" line in the journal was referred to once (except in Final Mix). I think it would have been much more charming to have more CoM references and maybe even Sora meeting Naminé rather than her just appearing for Roxas to talk to. Riku Replica wasn't even mentioned, which, while somewhat understandable, is kind of lame considering his importance to the game's plot. A journal entry would have been nice at the very least.
And Naminé's character seemed to pull a complete 180 in my mind. She just seemed like another Kairi, and I hate how they pushed Roxas/Naminé just because they're Sora and Kairi's Nobodies. They barely even knew each other. I think in general the game could have been more subtle about implications, anyway. BBS had practically no romantic hints for its main cast, and I liked that.
Moving away from story, there's the gameplay.
While reaction commands were fun in their own right, you could perform them simply by button mashing. There was no challenge.
Furthermore, you lost a lot of awesome abilities from the first game (except in Final Mix), like Dodge Roll, strike raid, arcanium, and so on. Drives were another fun concept, but also made things a bit too easy, if you ask me.
Cure was an insta-heal that sapped up all your MP, and you had to wait for it to come back. I preferred it in KH1, where different levels of cure healed different amounts of HP, and you could regain MP by getting hit or attacking other enemies. The absence of sells like aero, gravity, and stop was also a shame.
But honestly, the battle system wasn't that bad. I enjoyed it for the most part. It's the rest of the gameplay that honestly bugs me, other than Gummi missions, which were an improvement.
The world layouts were just so linear. In KH1 you could explore the worlds, interact with them, and they were just a lot bigger. There were puzzles you had to solve, and fun little bonuses like trinities and dalmatians.
KH2 took all that away. There was virtually no platforming, and you just went from one area to the next, fighting enemies. That took a lot of the fun away. I adore Hollow Bastion in KH1 because you can just go on a jolly romp, enjoying its massive environment, and the map was initially a huge challenge. TWTNW...was not. It had no real puzzles to solve. HB was basically the climax of KH1, and it showed. KH2's climax was just cutscenes and battles. :/
tl;dr: Sloppy story, linear worlds, and easy gameplay are my biggest qualms.
...Though I do like the new stuff in KH2 Final Mix. Cavern at least has some platforming, which is fun to play through.
I can appreciate the pacing a bit better now as it's not like the Disney games were detached completely from the plot - they were a means to an end.
Spoiler