A common thing I noticed with TMNT cartoons lately is most of the long lasting villains of the show become allies by the end of it.
The 2k3 series had Karai and Bishop, and to a lesser extent Baxter, as villains throughout most of the series. By the end of it Karai and Bishop had become the Turtles friends and worked alongside them, and Baxter had been promised a new body in the future by Bishop who had become the president of the Earth. During Ninja Tribunal we had Karai, Bishop, Baxter, Chaplain and even Hun all working with the Turtles to take down the Demon Shredder. The Turtles even invite Karai to April/Casey's wedding with Dr. Chaplain, and Bishop watches it too.
Then in the Nick series, long-time enemy Tiger Claw declares a truce with the Turtles, and even Nick Bebop/Rocksteady turn a new leaf and decide to become heroes after taking out the Technodrome. Even Fishface was left upon on peaceful terms. Only Rahzar/Chris Bradford stayed "bad" until the very end and that's why he had the worst fate of them all.
Even in the original cartoon we're told time and again that 80's Bebop/Rocksteady aren't really bad guys, and they work alongside the Turtles in some episodes.
Do you think this is a common theme? When a cartoon is airing we're always like, "Oh I wonder how the villains will finally be defeated for good in the final season," but other than Shredder and some other evil villains, a lot of the other long lasting ones become allies.