Superman and Batman's outside underwear. Yeah, I know it would ridiculous in real life but so is Wolverine's yellow and blue costume and he's still wearing it!
I can't really explain it, but without the outside underwear they look....naked for some reason. How are criminals supposed to be intimidated of Batman when he looks like a pantsless Ken doll?
The "outside underwear" had a visual design function: To break up the blue of Superman's costume and the grey of Batman's costume. Without the areas of red and black to break up those large areas, the costumes look even more "painted-on" all over than ever, thus creating that "naked" look you mentioned.
But let's face it; this is all part of their idiotic "change for change's sake". If Dan and the Gang were REALLY worried about what looks ridiculous, or even had a clue about good design, Jay Garrick's DCnU costume wouldn't have been created...