I thought myself a little about base design :-) (yes a little), and I have an idea to consistently explain, why not so much guys are on the map, that no civilians running around in terror, and how the base layout can be small.
The PHALANX Bases should be (at least) two-layered. The upper layer with all the stuff, that MUST BE in contact with the surface, and a lower part, DEEP in the bedrock of the area.
The upper layer will consist of hangars, antennas, storage facilities for aircraft parts, fuel of the air craft and so on maybe a UFO-hangar directly at base (reducing the disassembly time and/or cost of an UFO), Ground2Air and Ground2Orbit base defense, automated ground defense and security facilities (including storage), where soldiers can be stationed just like on aircrafts.
The upper layer is connected with the second layer, that may consist actually of several of underground base buildings, by a long deep heavily armored elevator and of course a bunch of secret escape tunnels no one will ever find - a little bit like in stargate :-)
The underground layer consists of workshops, giant computers to analyse the radar sensor readings, internet,the hive mind link etc., the housing for all personal, laboratories and storage facilities, and in the very last corner the command center and the reactor :-) - ah and also a very BIG bunker with rooms for the civil personnel. Maybe some well places blockade points where soldiers would have strong defense positions.
When a base is attacked, first everything happens in the upper layer, and the N soldiers (where N are all soldiers on duty at the upper layer) fight against the alien intruders. The aliens might raid or run amok a little and damage/destroy aircrafts and stuff, maybe destroy the defense. In the later game, if you can't take down an attacking UFO, maybe the aliens decide to bomb the whole side. Either way, if the aliens can manage to win the upper level, they will come down to the lower levels, where a second fight will start.
In meanwhile every civil personnel is evacuated through the tunnels or into the big bunker. The rest of the soldiers also had plenty of time to equip themselves and got in a decent defense position. parts of the most expensive equipment is sealed (so that the aliens might have to shoot several times at the doors to open them). If they really go for the lower level I'd expected the aliens to have several waves, coming in every 2 or 3 rounds, fighting their way from the central elevator in every direction.
For a good and hard fight, and for making an successful bombardment something you can go on with, the stuff in the upper level must be very ... cheap or easy to replace compared with the lower level stuff, and the civil personnel must be the crown jewels of the whole base. So that you really don't want the guys in the bunker to die - and you don't want the aliens to blast the reactor...(maybe the bunker and the reactor should be placed on opposite sides, and elevator right in the middle, when a new base is founded).
So that are my little thoughts about base design.