Here's another one I did not like when I was a kid, but just finished watching and really enjoyed. The sets, such as Mombi's tower, and the Nome King's ornament room are amazing, and the story is very well done also. And it's scary!
I wondered why I did not like it as a kid. As a kid, I thought the claymation FX were kind of lame. Another issue is that the escape from Mombi's is extremely intense (scared the carp out of me as a kid) and the movie's climax doesn't capture the same level of fear for the characters.
Looking back, though, the good so outweighs a few minor quibbles that I can state with certainty that what I hated as a kid was the simple fact that it did not live up to what I thought a sequel to TWOZ should have been. My old childhood pals, the Tin Man, Cowardly Lion, and Scarecrow are basically left out and replaced with a new squad, the characters looked different, the Emerald City looked different and so on. In other words, I simply couldn't enjoy the movie on its own terms because I brought a lot of my own wants to the show.
Regardless, I was over it watching it as an adult, and I like it as much or more than the original. So, if you haven't seen it in a long time, give it a spin!