Interesting idea. If possible, I think it would be cool if the alien invasion force has already occupied most of the world and the X-com forces are a clandestine group working to overthrow the alien overlords. Initially, the X-com forces would be launching raids (ie replacing the current terror missions) where they have a specific objective (eg destroy the power plant; grab the guns from the armory; etc). Instead of radar, bases would be more interested in installing camouflage technology. As X-com succeeds at more missions, countries could revolt, bringing more funding (and perhaps a free base or planes or troops) and then the player would be tasked with defending against attacks on their newly liberated territories in addition to making more attacks on occupied lands with the ultimate goal being to free the entire world and drive the invaders back into space.