I don't post much (if at all) but I have been thinking about why ONLY Shredder and Heffer were cut from the roster, and I don't think it is as random of a decision as many people online are making it out to be.
My working hypothesis is that the '87 version of Shredder and Heffer have unique properties to their models that clashed with the current version of NKR3's bike and kart customization system. I will explain my reasoning:
Shredder
One of the most iconic design elements of '87 Shredder is his long and flowing purple cape. Getting the cape to collide with and rest on all possible vehicle parts and have it not be glitchy (important when you are almost always looking at a character's back) would have required its own physics programming for just a single character so it wasn't seen as worth it.
If the game only featured karts then Shredder could simply sit on his cape and that would solve the issue, but the game also has bikes so that makes this an impossible solution.
They could also just remove the cape altogether like the 2012 version (who often fought without one on his show for similar reasons) but we all know Nickelodeon is very overprotective about changing iconic character designs in their licensed video games and this may have simply not been possible.
Heffer
He is a balloon-shaped heavyweight in a game that doesn't currently support this kind of heavyweight, simple as that. Reptar might also be a big guy height-wise but he isn't round like Heffer is. Reptar follows the "rules" of being scaled down enough to fit into any vehicle.
Kart racing games solved this issue a long time ago, but the question for the developers here is whether it was worth it to adjust things like vehicle scaling for just a single character that would need this enabled. For them it was not.
Finally.......
Annnnnnd that's it for a fairly long post. I could somehow be wrong about this but the fact "weird" characters were excluded only in the game that expanded the customization possibilities for the roster makes me believe I am probably not.