I think the issue is going to be whether or not you go to the ground and have to grapple. If you can keep keep him at bay, then his nakedness doesn't matter much but if he's got BJJ or wrestling experience, you're in for some balls in the face.
Vulnerability to biting aside, being naked prevents one from being easily grabbed (clothes, etc) and allows for full range of motion so it's somewhat more advantageous. Plus the clothed, inhibited fighter will likely not bite because that's bordering on foreplay.
Honestly, if the naked brawler is a purist then your best bet is to scatter some broken glass around, but if his style is less strict and he's wearing shoes, then you're doomed if you can't knock him out in a single punch.