Oh, you know what else? A, like, full-scale X-com.
The xenos are invading in full force, sending down armies at a time in fleets of UFOs, maybe using Star Trek style teleporters and whatnot, not just little task forces in little landers. Not just terror weapons, they'll eventually send down battlesuit power armor things, force-fields, full-size tanks, flying things like drones, jetpacks and weapons hoverplatforms, and possibly have support from the motherships in orbit (orbital lasers?) and/or UFOs on-scene. To combat the alien menace, you have field several Skyrangers worth of squads, have spotters and air-support, similar vehicles, possibly artillery deployed outside the combat zone. Drop some spotters and snipers on a skyscraper or apartment or something blocks away, but if they figure out where you are, be prepared for shelling. Skyranger crashes in hot territory, you need to defend it's position with the survivors while reinforcements come to save 'em. Oh no, a giant robot/monster! After the first one stomps you and you're forced to evacuate, research and build a counter - do you make your own sweet robot, or just a crapton of planes with missiles? The President/whatever is under attack! Are you a bad enough dude to evacuate him?
Speaking of, I'd like to see some kind of infrastructure and political game to it, too. Build (possibly underground) railways to speedily transport heavy equipment without the use of a Skyranger, or for stuff you can't stick on a plane. I have the idea of an "X-com embassy", with bureaucrats and stuff arguing to keep the countries from falling under xeno control, increase funding, and doing stuff like maintaining the infrastructure you build in whatever city/country they're assigned to, and drilling the local populace and law enforcement to speed up evacuations and taking shelter - maybe acting as a go-between to arm said law enforcement with cool X-com tech. They'd be protection targets during city raids, since they're not likely to be in armor, or trained like your soldiers are.
Also, pilots. Statted pilots, like your soldiers. Now, skill will allow outdated planes to at least stand a chance against superior aircraft, though there's always the chance that asset will die if he gets shot down or send without wingmen. Veteran air-support pilot gets shot down in the combat theater, get your guys over there to save him. Skyranger pilot gets shot! Unless your regular soldiers have some piloting skill, that one's not going to be able to evacuate anymore.