I <3 the last idea you posted, where were you planning on going with it? :)
I got the idea from the Turtles Forever movie. Shredder finds out that there are multiple dimensions and universes and different people in each of them. He realizes there are thousands of universes that have their own version of the Ninja Turtles...I was thinking that instead of him off the source of the turtles (cause that would destroy him as well) he instead sends them to a place where they don't exist. Instead of it killing them, it just turns them human.
They would end up in a modern place (not the kind of modern they are used to, but our modern world). A much more 'peaceful' place than there are used to. With the down time of being stuck there, they get to enjoy time as being a human. But then Donnie finds a way to get them home and back to being turtles. There could be a number of reasons for why they have to go back (being heroes is a big job after all), but it's hard to let go of being accepted.
The game itself would revolve around their time as humans. They would end up in New York (since that is where they would be coming from) and can use the bit of money they have one them (cause for some reason they always seemed to have a little money in the shows) to get a hotel room at first.
I would need either my partner to play the four guys or play four Original Characters. Or I would play two of the guys and my partner play two of them. I foresee lots of fighting between them and the outside world due to their social awkwardness.