I think I like the minimalist approach you posted best. Your names look fine to me. I especially like how you added Nails in front of toe>fingers. I don't really see the advantage of adding numbers in front. It's actually mildy annoying to look at ( my brain wants to look for Skin,Nails,Eyes etc.) and the numbers get in the way. Doesn't really matter I guess.

I think maybe you should add a true cornea. I don't really see the point of a full eye surface ( is it for teary eyed shaders and such?)

You are correct about Blender only allowing 16 materials. I think they may allow for more in a future release because it's one of the main things on people's wishlist and complained about often.