To be honest some of them weren't that out of place. Silver was a mutant ape, Bonesteel was a human bounty hunter, Dragon Lord and his people were from another realm, etc.
Those characters could have fit into either cartoon, but I can see why nothing from Next Mutation is allowed to appear in any other TMNT canon.
I see the Nick series taking some classic 80's cartoon characters, maybe some 2k3 characters like Hun and Bishop, and some comic characters for their villains.