Probably because it looked dumb. It never made any sense in the 80s show why his android body had a human-esque appearance. It seems unlikely that's what Krang's original body looked like and it wasn't human looking enough that he could pass among Earth's populace if that was his intention.
If there was any other reason other than it looking stupid I imagine it was because half the head gets cut off. They probably didn't want kids getting the impression the turtles had beheaded an actual person and not a robot.
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