if I remember correctly, the game explained somewhere that your craft would take off before a base attack... perhaps it would be cooler to actually have them in their respective hangar unless you manually evacuated them. hangars were indestructible to avoid the "orphaned craft" problem, I guess. imagine your base being attacked while your skyranger is still returning from a ground mission... if the hangar is destroyed, it wouldn't be able to land. same thing applies for "repair time" penalties, of course.
I guess a "repair cost" penalty would be fair, though. it would certainly make the base defense more interesting if your troops need to be more careful with explosive ammo of any kind.
Another thing is that in your base defense you should have "civilians" - your scientists and engineers! it would make base defense facilities more valuable - trying to avoid base defense missions, because it endangers your staff.
while we're at it, perhaps the base defense facilities could become more useful if the result wasn't purely dichotomic. what I'm trying to say is: imagine your base is attacked, your plasma defenses hit the battleship several times, but barely fail to destroy it. shouldn't the attackers at least have suffered some casualties? instead they always come at you full strength.
at the same time, if your base defenses shoot the ufo down, it should crash and appear as a geoscape crashed ufo, right?
