As mentioned in Blues post, you will find weapons of varying visual style. I was thinking that there could be a way of changing the style, perhaps an NPC that you pay a little bit of money and it would let you choose which one you wanted. This would mean that if you find a weapon with stats that are particularly good but the visual style is not to your liking, you could change it without having to find a new version of that weapon to do so.
This may turn out to be in the final game, and if not I'm sure that at least changing the colour will be as they have already mentioned that. Personally I think I'd prefer it if you couldn't change the style though. It would just make the procedural generator a bit useless in the end.
I think You should be able color your equipment. This way Girls can have their pink armor and weapons and guys can tell each other apart in multi player.