Two stages would be too tedious. The more concearning fact is not that it will take time, but ammo. If you have to play through two phases of it with the puny stats X-com soldiers usually end up it will not be practical to carry arround enough ammo, except if you have dedicated ammo mule agents. Which is ridiculous.
Except if its possible to allow durring the transition phase a requip based on the stores and looted equipment. Speaking of which as I remember from TFTD, unless you pilfered the items/corpses/stunned aliens to the exit grid manually, there were no recoveries from the first level.
Regarding the battleship above the base, while I understand the sentiment, I also understand why they actually didnt do something like that in the first place. After the ground force gets wiped out why would the ship remain on site?
I support the idea of a ground level with certain camouflaged (so to speak) structures but:
Given the fact that X-com agents are hunkered down inside the base and "All x-com personel and craft have evacutated the base as per standard proceedure" x-com agents should spawn underground only, and since the attack is the underground base itself the aliens shouldnt have (IMHO) a considerable presence on the ground. Except if you do it another way: Spawn them up and have them move through the access areas down, but I dont think that the engine can give aliens directives.
