So what's the point of showing the monsters still being alive at the end?

[victory_angel]

I believe Ciro said that not all mutated characters would get happy endings.

And with the time being spent with Timothy right now, it's still possible to restore him, the longer they take the less probable it would be. Part of this has to do with Roger Craig Smith being impossible to get a hold of, otherwise they would have had him more.

But the attitude of the turtles towards Timothy is like "He's not going anywhere anytime soon, so we'll cure him next time." And it's plausible that Mutagen Man has a darker purpose, particularly with Donnie's character development. Since it was heavily emphasized that Donnie was responsible for whatever happened to Timothy since had chosen to take him on as a student.

The Chimera (Turducken) was assumed to have been killed. We know it's alive and that it's terrorizing Northampton. But when they escaped they pretty much assumed it was killed off. So that is likely a character we will see again.

Dream Beavers...will also come back since there is more then one Friday the 13th film. So it is possible they could return and terrorize the Turtles and Co again maybe the mutanimals. But it's also possible that they could come back as Anti-heroes and haunt the nightmares of the more villainous mutants.