Best Turtle - hands down Leo. He was just amazing in this series. Leo has always been my favorite, but Nick Leo just brought a lot more to the table. He's adorable, compassionate, a strong leader, geeky, and the list goes on. I didn't mind any of the voices for him, but Seth grew to be my favorite one of the three.
Best secondary character is DEFINITELY Splinter. I loved his wit, wisdom, and cheeky moments. He's by far the best Splinter in any incarnation out there. Hoon Lee did an amazing job with him.
Worst Turtle is Mikey. Ugh, I wanted to like him, but he was so inconsistent in this show. This has been a problem for me since the beginning. When he shined, he shined, but the moments were few and far between. Cipes is wonderful for his character, though. Just wish they didn't dumb Mikey down so much.
Worst secondary character...hmmm...that's a tough one. I liked most of the characters pretty well. Some had to grow on me first. Even Casey grew on me, but he did have some ill-timed outbursts that drove me nuts.