If you allowed moriarty's single large base idea, could the additional base slots in base view (where you can move between base-1 and base-2) be used to represent different floors of the same base? In essence hack it so all the different bases are actually the 'same' base, in the same location, sharing/pooling the same research/manufacturing/storage capability, and using a single multi-level battlescape when under attack
I think this is a great idea, but it would be very difficult for base defense missions, don't you think? If you want it to be a multi-stage mission (like TFTD's alien bases), that would probably be possible, but where would you start? sure, the aliens will come down from the top level, but they would probably move down the main lift rather quickly, so you would basically be fighting on all levels simultaneously...
of course, it would be interesting to start on the bottom level with only some of your soldiers, then once you cleared that, you will join the soldiers one level above that who until then were holding the aliens off (a.k.a. nobody died, perhaps some wounded on both sides), and you have to fight your way to the top level. kinda complicated, truly epic-scale if done right, but then again, in this kind of game it would be your
only base, so that would suit the situation just fine, I guess