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The Shredder's one true love is power and control. And at the end of invasion Tiger Claw had said the City was theirs.
So mutating his followers in a way of dehumanizing them because animals can be controled. And also the humans of the city won't see them as people, they would see them as beasts and monsters.
So in other words
Shredder is the Damyo if not Emperor of New York City.
The unmutated humans of the City are is subjects who live in fear of his wrath.
And his mutant army and his foot bots are his grunts who to enforce the Shredder's law and judgement upon the citizens of the city.
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