I wanted to say that I don't like the idea of using exactly the same weapons like the aliens use, or captured weapons. Where is the element of inventivity and creativity in that, if you are looting and using the loot to kill the aliens? It's perfectly ok to use their tech against them, but as Winter said in a post, it's highly unlikely that their weapons will be usable by humans. Just replacing a handle and a trigger mechanism doesn't require to many brilliant scientists. So I would preffer a human made weapon based on alien tech rather than the same weapon aliens use.
As for the customizable weapons I wasn't thinking of something to complicated. You could adjust the damage done, rate of fire, TUs, range, etc... but not the graphical model (like in Gal Civ). Ofc you have to think of some limitations, like if you increase the damage you lose range, etc, and some attributes can't be changed, depending on weapon and so on.