But yeah, I see what you mean. Seeing as they already had seperate models for the skirts and the trousers then why not make them seperate items?
Because they only had two separate meshes. In order to have it so that men could wear skirts and women wear pants, they'd have to have four different meshes, and a way to determine which one you wanted.
When your character puts on a pair of pants (or a skirt, or what-have-you), he doesn't actually place a clothing item on top of his body - that part of his body is replaced by the clothing item, which is its own mesh.
It's easy enough right now to set it up in the CS so that, for instance, male characters get the skirt version of an item rather than the pants version. But that male character is going to end up with a female body, because that's the only mesh there is for a skirt. In order to make it so that male characters could wear skirts, they'd have to create a male skirt mesh.
I wouldn't be surprised if that's just what they end up doing though - rather than having skirt and pants versions of the basic clothing, they'll have basic skirts and basic pants, with male and female meshes for each.