From what I've tried and tested, you shouldn't worry about a limit on the number of skins. I've been chucking loads of variations in to test stuff. I'm not sure if there's an upper limit somewhere, but I don't see anything that suggests you couldn't have tens if not hundreds.
My only thought on having loads of them, is whether it would start to slow the game down if they were all on the same map at once, or even simply having them loaded into memory would slow things down. I've not so far managed to put any non-player 3D characters in my tests, so I've never had more than one 3D person in game at once.
Also, regarding skins - we might have to tweak a lot of them once the shaders are a bit nearer completion. If we've got a more fallout-like light and shadow on each model, we will probably have to adjust the colour, painted highlights and overall brightness of a lot of them.
If you look at this image :
Basically, we're aiming for that 3D guy to look identical to the other guys around him. Obviously we could adjust the colour and painted highlights now, but once the shaders are in, we'd probably have to do it again.