I wanted to pick one of the other brothers just to say "What a twist!" but in the end I feel it's up to you, but while I think it should be your choice alone I guess I do have some thoughts on it. :3

For me, I feel TMNT is a weird universe, well, most fantasy universes are a tad surreal but especially for TMNT, I dunno, I'm not a massive fan on it now but I feel that in that specific universe the topic of reproduction with mutants should be taken in a way that makes sense in our world. What I mean is, the mutants are either mutated from animals or humans right? If that's the case I feel they would become almost completely unable to reproduce because well, they can't mate with individuals from their old species or from the one that they came into contact with during mutation because they're now of a different species, meaning that the only individuals they could mate with would be individuals who match them in regards to their biological forms (for example with Aelita, it would be a male mutant who has taken the form of anthropomorphic domestic cat), otherwise it wouldn't make sense.

Anyways, that's just my thoughts, after all, the explanation for the mutants in the first place is science goo I think, so I guess stretching imaginations to crazy levels isn't unheard of in the universe of TMNT and I'm just trying to force it back into reality too much XD, either way, it's your choice 100%.