Exactly what I have in mind! Some more ideas include:
- Cloning facilities: large, heavy duty cloning vats to breed Mutons and Chryssalids, as well as smaller vats for Sectoids and Floaters. Embryonic, half-formed aliens can be visible inside.
- Industrial-sized surgery rooms (using similar or the same equipment as the Abductor) for installing all those cybernetics in freshly bred Mutons and Floaters.
- Manufacturing plants, with suggested production lines (and perhaps some extra alien weapons/equipment to capture).
- Medical facilities, containing cloning vats (much like ones in the cloning facility above, but empty) and a monitoring computer.
- Dormitoria, where aliens spend their "free" time - when not on duty or at the entertainment station (which is a lot of time). Include casket-like "beds" (possibly filled with some fluid) and maybe feeding stations (simple machines which apply dissolved alien food to the bloodstream).
- Perhaps a human tech room, with some Earth-made equipment (for studies or some other, more mysterious purpose - supplying their human/half-human agents?).
- If we want to go a little further, UFO hangars (only for small craft for emergencies, like Commander evacuation or special assignments that come up without warning). With a functional Medium Scout or several Small Scouts inside.
Making and coding these in should be fairly easy for an experienced modder, and I think they'd add a lot to the game. Even I could give it a try, at least with the graphics. 
Maybe also making alien bases unique to the race?
Sectoids would have very clean looking cloning chambers and Cyberdisk engineering rooms.
With maybe also a lot of alien entertainment.
Missions of interest: Research, Abduction and Harvest. (not limited to)
Floaters a bit more messy cloning vats with more integrated engineering rooms to add the anti-gravity device to freshly cloned Floaters.
Bigger cloning vats for reapers.
Missions of interest: Research, abduction and Terror. (not limited to)
Snakemen would have room full of eggs and artificially kept alive humans with chrysalid eggs in them maybe even some hatching during a base assault? XD
Barely any engineering rooms
Missions of interest: Abduction, Terror and Harvest. (not limited to)
Mutons alot of human body parts, alien surgery and genetic manipulation equipment. (I see the original Mutons the result of alien experiments on humans)
A lot of alien food containers as Mutons need their food to feed those muscles... ^^
Missions of interest: Abduction, Terror and Retaliation. (not limited to)
Ethereals are similar to Sectoids, with most of the entertainment replaced by unknown and mysterious psionic devices of some kind.
Missions of interest: Infiltration, Research and Retaliation. (not limited to)
