Donatello was always my favorite, probably because he was the smartest, I'm just drawn to intelligent characters.
I've never sat down and watched this whole thing, I really should though because I always thought it looked fantastic. My favorite thing about it are those interview segments like this one:
http://www.youtube.com/watch?v=ZnOzv55JVGY
I don't even really look at the whole thing as some really botched braindead attempt at exploring and milking every single possible outlet of the franchise to creative death. I just kind of like seeing how absolutely overblown they took the stereotyped characters that the turtles became. In the cartoon, they already had a bad enough stoner surfer vibe. But in this thing, they just take it so much farther beyond ridiculousness. It's just a massive exercise in 'ok, what's the absolute farthest that we can take this cowabunga pizza thing?' and they take it pretty far, DUUUUUUUUUUUH!
But whatever, Turtles rule, I'll love em forever. I still fucking hate the way Jim Lawson draws though.