There was a bit of discussion on base defence in "Symbols for the geoscape" thread, I think this is better place to continue.
I support this but there is one problem: Will the the squad/soldiers in this base be able to grab some equipment before the mission starts or is it necessary to take this into account before an ufo is able to land near you? If I employed 10 soldiers in this base it would be unrealistic to handle two of them as civis. I guess I'm raising a complicated matter.
So, in general, the question is - can soldiers not assigned as dropship landing party take part in base defence? By now the only way to equip your soldiers is through Aircraft menu. And if I want to garrison a secondary base against alien attack, I have not only to build living quarters, hire soldiers and buy them equipment, but also build large hangar and buy a dropship, even if that combat team is meant for base security only.
This could be handled in the same manner as in UFO:ET, when you equip soldiers right before the combat mission and all combat personnel is available (or the first n soldiers, where n - maximum team number). In this case there should be a way to equip them outside aircraft and equipment should not be stripped off if a soldier is removed from dropship crew.
The other idea is building a sort of security station on the base and assigning soldiers and UGWs there in the same manner as for aircrafts. In this case, only security personnel defends the base, while aircraft crews, well, perform regular aircraft maintenance.