Why not create a multi-layered base? Put a building restriction on what levels a hanger can be on, but allow a commander to punch down another rock strata to build a "second" base below the first. Programming wise, a second base's class(s)? would be 90%? pointers to the first base's class(s)? The interface would not be any different, save for a sorting function. (PHALANX HQ - Floor 1, PHALANX HQ - Floor 2)
For the most part the game would "see" these same bases, one just being the pointer to another, as the same base. Require no extra mechanics, save maybe a extended entrance tile leading to the level below. Before you ask, no, I'd love to have the time learn the source and code that, but don't. Classes are only slightly less of a time suck then World of Warcraft. Just strikes me as a easy, if testing intensive, mod.
Maybe instead of each craft having it's own hanger, be able to (build/research) one that had the one large landing pad, but could be lowered to a lower level and be rotated out with other landed craft or empty pads. Something vaguely similar to a air craft carrier's lift. Saving a base where you wanted to field more then just the Firebird a large part of the floor plan.