So, I am further along in the game and my main hero is a level 30 sentinel and I just made a second superhero to see what it is like playing as a blaster.
Anyway, in designing her costume, one big drawback I have run into is trying to give her a belt. She wears a sort of waistcoat but for some reason, the costume designer puts the belt over all of her costume layers including her coat.
I know that the costume designer intentionally does this, but there is an online superhero-making engine called Heromachine that lets you make 2D superhero characters. It is pretty basic, but one thing it does let you do is choose what layer of a character's costume is displayed and where...so you can bring different layers in front or send them underneath before finalizing and flattening the hero's design when you are finished.
How difficult would it be to do a similar thing in the costume designer? I do not think that you would need to maintain the separate layers in the actual game, but just have the ability to bring them forward or back during the design process.