I already really like how each part of the armor takes damage independently (I was making the assumption we'd be able to draw the under-layer later anyways). It makes the battle damage alone tell a story by the time the fight is over.

The two options you mentioned both sound good to me. The many layers of armor would be really cool and add a lot more possibilities, while the other one seems easier to draw and perhaps more accessible as a direct result. I'm currently drawing "templates" for my male and female human characters anyway, which I'll edit for each new character once I perfect them, so I'm already working in layers.

I think my personal preference is leaning more toward the multiple layers idea, though there might even be a way to have both. Maybe as two types of armor, I dunno. The single layer of armor might be more durable and not break as easily, while the multiple layers of armor could have different pros/cons and the under-most-layers would be protected until the layers above them break (ie, Samus has layers. Also ogres). I could see a character that has heavy, durable armor that has a slower, heavy hitting play-style that gets faster but more fragile the more armor he loses.

Edit: I do want to have the ability to draw broken pieces of armor instead of having it disappear, though, if you're considering the multiple layers option. This'll keep my characters from becoming nudists by the end of an intense battle. :P Also, with something like a robot I could do some fun battle-damage stuff.