I'm starting to warm up to TMNT 3, I think the story, action, and humor trumps TMNT 2, it's just the costumes that make it groady.
Methinks TMNT 3 > TMNT 2. Really.
* better fighting scenes - and the guys are using their weapons! TMNT 2 had mainly hand-to-hand combats
* better storyline - what bugs me about II is that scriptwriters came up with some ideas but solved them in a quite lame way. "The Secret of the ooze"? There was actually no secret of the ooze and that was SO lame! :| Also, Eric Reyes Jr was neat but kinda useless - his character has barely any impact on the plot
* better OST... :P I really like III's music way better than II's.
* Casey is in III :P BTW - I don't understand why he's not in II. I suppose the action in II takes place only a few weeks after the events in I. And Jones just disappered, leaving me in sadness and grief <as I wanted so much to see April and Casey's wedding in the end:cry:>
I think the reasons why most people hate III are those freaky costumes and the atmosphere that totally differs from the first two movies. I and II in their darkness are very close to Mirage comics, whereas III is pretty joyful, that places it much closer to the old toon in my opinion. If someone loves the first movie, he'd naturally prefers II rathen than III, although II is not all that that great in fact.