It may sound like a borrowing from UFO:Extraterrestrials, but I would like to suggest SAM-sites and other ground-to-air defences being vulnerable to aircraft fire, along with alien bases having such structures. So that a raid on alien base could be either preceded by an airstrike with attack crafts, or player tries his/her luck with sending a dropship against unsupressed AA defence. As an option, only planned "external" SAM sites and radar towers could be vulnerable, while base's own defences are hidden below the ground and thus indestructible.