Game Informer had a pretty good interview with one of the X-Com guys, and they brought up some really points.
I can't remember all of them but I know one of my favorites was the ability to get heavy weapon (even if they were limited) and straight destroy the enemy.
Air support would be really nice--or they could at least have a bit that explains why we can't just carpet bomb some of the downed space ships.
Defense--not just base defense, but it'd be fun to have to defend all the workshops you build. It'd be fun to be dropped into a zone and have to defend it.
More customization. I can really only choose between (at least for caucasian) Norris God, Jonah Jameson, generic white guy. I'm already playing Norris God, but I have more than two white friends.
Also, the ability to change gender and nationality would be so much better, I was surprised to find it wasn't included.
Do some thing with the SHIV. I really felt like it was a waste--I didn't have that many engineers though. It was expensive, super inaccurate, and got shot all the time because it couldn't use cover or duck behind walls. I think it should be that the SHIV can't "die" just taken out of service and repaired aftered the mission--after a long time, and with a possible cost.
Fix the graphics pop in problem. There's no reason it should take so long to render the holo-globe.
More mission types--in addition to defense. Deffenately would help with long play.
More research branches. Research is one of the key parts of the game there should be more to do.
A suburbia ("Nuke Town") style map would be really cool.
One or two large skirmishes would be really cool.
Steal some ideas from Evil Genius. Maybe have to change base locations, or gather representatives from different countries.