Michelangelo is considered by the fans as being either funny or annoying. He became even more divisive with the fans after "The Croaking". Some fans felt sympathetic towards him in the episode and were happy he gained a friend while others felt like he was acting like a spoiled brat and think the punishment he received at the beginning of the episode should have increased ten fold due to his actions.
Casey Jones is divisive among the fans. He became less so as we learned about his personality and motives. The fact that many Apritello shippers jumped the ship around the time of his introduction probably helped. However, some of the fans are turned off by his antagonistic behavior towards Donatello in season three all because he likes the same girl he does. Others are put off by how often Casey seems to shrug off devasating events (such as "Annihilation: Earth!") in favor of commenting how awesome their adventures are or whining about how there's no action happening to the group at a given moment.
Donatello himself became divisive among the fans due to his crush on April. Fans either considered his crush on April to be cute or Squick. His crush on April was initially viewed as cute and even endearing during the early part of the first season before it suddenly stopped being referenced to for a few episodes and then it came back and became extremely flanderized. More focus starts getting put on it and we get to see Donnie makes less than rational choices because of it. Then, there was "Operation: Breakout"; Raph tells Donnie to leave him out of his attempts to impress April (Raph clearly didn't like being used like that and was offering some advice he seemed to think was helpful). So what does Donnie do? He basically goes on a VERY dangerous rescue mission by himself without telling anybody to get April's dad away from the Kraang. Not only that, but he almost gets himself and Mr. O'Neil killed multiple times. All to impress April.
Raphael is divisive with the fans due to being a bigger jerk in this series than he's usually depicted. This has cooled off a bit though, thanks to getting Hidden Depths and toning down his behavior in later episodes.
The Shredder is divisive among the fans for his personality in this adaptation, where his sole motivation is to kill Splinter. Some love the portrayal and how ruthless and determined he is to the point where he literally stabbed Splinter in the back even though it meant the end of the world, while others feel the show has heavily flanderized his character and miss how he was in the previous adaptations where he had other villainous ambitions in addition to wanting to destroy the Turtles and Splinter.
The Kraang are either an interesting part of the Big Bad Duumvirate, due to their connection to the Turtles' creation and their Hidden Depths, or they're just boring and generic with an annoying speech impediment. There is also a third group who argues that they were interesting on paper, but suffered too much from Motive Decay over the course of the show.
God-Mode Sue and Creator's Pet.