I love TMNT III. It's way better than SotO. At least the third film has a coherent story line, better characterization and better writing overall. I don't get all the flack the third film gets. If you compare the second and third films closely, there are so many more holes in SotO. Like a previous poster said, SotO was basically a sequel to a kiddy Turtles movie that never actually happened. That's the #1 glaring fault with film two - it tries to pick up where the first, dark, gritty, well written movie left off. But it could never do so, because of the execution, because of the nonexistent explanation of what happened to key characters like Casey Jones, the change from Hoag to Turco, the cruddy change in Turtle suits. Why did they so drastically change Donatello's look? It was just a huge fail for me. His bo staff was a kid's toy. The story with the origin of the ooze had potential but it was bastardized and straight up poorly executed. There's also a lot of carelessness in the production. For instance, when Tatsu starts busting stuff up in the junk yard, you clearly see this little punk who was lucky enough to get a spot in a Turtles film smiling like a fool because he couldn't control himself. And the film crew did not spot this? Ha.
TMNT III excelled with better story and plot, real character development for Michelangelo & Raphael, Casey was back, and there are truly comedic moments in that movie, especially with the honor guard and Casey back in NYC.
Plus, who doesn't like Turtles in feudal Japan?
All in all, SotO is waaaay overrated, while TMNT III is way underrated.