I was looking at the new Character Studio export stuff and looks very flexible. Here are some ideas I have, yet to try out, but should be possible.
1 - Using the weapon add to BIP segment, to add armour etc to the character.
2 - Having different base character meshes on different layers, which refer to the same BIP data. (keeps file size down & easier to allow different player switching)
3 - This looks like it would be a bit trickier, as the Weapons are just a PRO file added to a BIP segment, you should be able to have more complex animations of the weapon firing(I think you would then have to manually override the entity anim frame for the weapon each frame & write your own handler for the weapon animation, but should be cool)

Cheers
Darrin