The way I saw it, mutating another batch of turtles with humans would give you a different "mix," so you'd end up with mutant turtles, just not the same kind of mutant turtles. I've also got a theory for the large number of mutants in the future, being that all those mutagen-filled sewers (and let's face it, in present day TMNT all you had to do to be mutated was go into the sewers)finally flooded, hitting just about everyone on the first few floors of NYC. You would think there would be more sea-creatures, but maybe they live mostly underwater, in the ruins.