OK, here's what I've noticed;
each iteration of the Turtles have them looking more "superhero-like" and less "toy-like" per the original TV series.
As the characters have morphed in a more serious appearance, the use of different colored bandannas to differentiate the turtles looks very childish, a-la Fisher-Price!
Along with a more "superhero" appearance, the turtles have subdued coloring on the bandannas, so now it makes since that skin tones can be used for a more realistic effect while making the boys individuals, an identity as unique as their voices.