Well in the original they didn't want to exterminate humanity but wanted to subjugate them like they did for the other races, the scouting missions are for researching humans then leading onto infiltration. Terror missions are to try and shock humanity into joining the aliens and the battleship retaliation missions are self explanatory, as to why they don't launch on a full scale invasion could be that they would have to deal with the regular military instead of just XCOM.
What I think would work well is an X-Com-type-game where the Earth is in fact suffering a large scale alien invasion and X-Com is more like a very-well-funded guerrilla outfit than a first line of defense. It would also fit the size & scope of the organization, its squads, and the scale of the missions you do, and the importance of the approval levels of the various continents (can they afford being caught funding a resistance group?).
Interesting, I would see XCOM maybe not as a guerrilla unit but special forces to try and defeat aliens behind enemy lines and you need to balance on what missions you undertake on how the global war is going.
Of course the way the IP is being used I wouldn't be surprised to see some XCOM RTS or some Civ style XCOM, although tbh the Civ2 XCOM scenario was quite fun.
It's not -quite- that way, but UFO: Aftermath is a game where the aliens have already won. So you are kind of building back up from scratch.
It's not very X-Com-y, though.
Oh god, the actual story of Afterlight and Aftermath is pretty horrible, gameplay is quite fun though.