No offence but the ideas so far are terrible or just trolling attempts, you can't "fix" the PD's TMNT movies, it is what it is. We already
have a similar thread but at that point it was a "what do you want to see" since the possibility was still open for a sequel.
You have to go with the strengths that the PD's interpretation offers granted that's not a lot but it does have one: a live action TMNT film where anything is possible including the most out there stuff in any incarnation including sci-fi. I wanted a third movie since in this version there aren't any restrictions on what they can't do. I honestly think this will be the only time we'll ever see the Technodrome or Krang on a big screen live action interpretation so I'd definitely want to see more of this universe do while not the fan favorite it would give us maybe the only live action interpretation of crazy stuff.
So what would I do? Let's take a look at what we were left off after the first two movies:
Shredder could've recovered from his transformers armor/defeat in the first movie but I don't think he could ever be a legitimate threat in a fight after being disposed of by Krang in seconds, talk about burying the main villain so I don't see him being a big threat any more in future movies besides being someone who moves chess pieces around. Sachs was completely ignored in the sequel and he should've been there, I mean as much as you hate him they took an entire movie to make him a part of the universe so he should get some type of closure even if just to dispose of him but to ignore like nothing happened. I'm pretty sure Beebop & Rocksteady would be back in some minor way. The Technodrome and Kraang I just don't see them in a sequel, I mean what else could they really do that they didn't do in this film with Krang?Drome to make it different? Baxter Stockman was obviously set up to return big in a sequel and he'd probably mutate but I doubt he'd be able to carry a film by himself.
I'd want them to try something totally sci-fi/fantasy heavy and craziest TMNT stories out there that would never be able to be done in a more "realistic" TMNT movie as mentioned above. And I don't mean time travel, that's not that out there but doing a Triceratons/travelling through space for whatever reason and have much of it not set on earth, some ancient Japanese myth come to life with lots of magical stuff in it, or even better an all out mutant fest where we see all our favorite mutants all in one movie that we remember from the toys or even other incarnations, this could be done through mutagen or by travelling to another planet or going to another universe through a portal made by magic.
Like I mentioned the redeeming factor in this interpretation is they can do things that most grounded interpretations wouldn't be able to do so they needed to take advantage of that in a third movie and play to the strengths. yes April would continue to be Megan Fox doing what she does best. None of us care if the hulk turtles do outlandish stuff after all, the universe was already tainted since the first film. I don't want a "city at war" story or whatever realistic "let's try to save the story and make it like the vision that we wanted", It was already too late for that after the first film and that should be saved for a much better interpretation of the turtles on film. Have fun with what they inherited.
For those reasons above I really regret not having a third movie, we'll have to wait a long time before we get a reboot that we actually want/love (most of the fanbase, never for you Andrew; sorry) so why not go crazy with a sequel and do things that would never be done otherwise.