When it comes to alien weaponry I really like the system X1 X-Division mod have. Each tier of weaponry have not just one but actually TWO types of weaponry. One of energy type and one of ballistics type. And just like X-Division operatives can and should use both types of weapons, so do the aliens. And they also have weapons resistances depending from it. Caesans, Wraths and Harridans use energy-based weaponry like phasers and plasma guns and heavily rely on energy shields for protections which are good against energy-based weapons. However they are poorly armoured and can be easily downed by ballistic weaponry. Sebilians however are very tought and armoured, extremily resistant to concusive force and ballistics but energy-based weaponry can make a short work of them. They also use a little better variant of firearms initialy because they are too dumb to be trusted more complicated and deliciate weaponry anyway. Their less intelligent friends like xenomorphs and reapers follow the same rule in inverse: reapers assisting sebilians are very resistant to lasers but are vulnerable to their handler's ballistic weapons. Sounds really reasonable in case your war pet suddenly turns on you, huh?
I think X2 could use similar system - sure, you can pick up and use alien plasma rifle (though poor ergonomics and unfamilar design will make it unconvenient), but the alien type using it will be very likely wearing armour designed to protect from it, so you are not getting much. However, the same plasma rifle could be useful against other aliens or against brainwashed humans/collaborationist forces. Actualy if I remember correctly in original X-COM laser weaponry were more useful against sectopod then plasma weaponry, because the latter had extremely high resistance to plasma guns which make sense.
It might also actually make sense for humans to use completely different weapon technology then aliens do. While aliens focus on energy weaponry, humans will focus on ballistics and maybe melee weaponry. Because the latter works better in Earth atmosphere or something like that. Humans are already incapable of psionics but field combat shields and batons that aliens do not - why dont we make humans even more different in their weaponry too? That will make aliens even more different and huh... alien to us and will allow for some more unique gameplay then original xcom.
X-Division also made it that instead of being sold enemy weaponry is taken apart for materials to be used in constructing the human counterparts. You take apart fancy alloy ballistic rifles - you assemble the brand new human alloy ballistic gun using the barrel and internal parts you got from them.