Honestly, the big difference between Xenonauts and the upcoming XCOM-Alien Unknown (to me) is the emphasis on reality and cold war era tech and mindsets. I'd love to add additional strategy into the game by grappling with political forces during the cold war.
My idea... (not nearly as well thought out and explained as your ideas, thothkins. Bravo by the way, on all those excellent ideas)
... is basically that the Xenonauts can be absorbed by a country or multi-national force, and gain and lose perks by doing so. So, say, Xenonauts becomes part of NATO. They will gain monetary and military funds, but lose soldiers, supplies, tech, and info from Warsaw pact countries. Or, Xenonauts can become part of an individual countries' force, such as, say, the USSR or East Germany. They will gain even more funds from that country of origin, more so that if they were to join, say, the Warsaw Pact, but will lose access to cutting edge equipment, soldiers, and info from friendly nations for "security reasons". I think it would match with the spirit of Xcom, because you will never be able to have everything (use of both the sputnik satellite program and NSA satellites would be impossibly useful, but politically unattainable) but will be deprived of the best toys if you stay independent.