I have had several ideas and I thought that I might as well as post them all in General.
I will number them so you can comment on a one or all.
I know not all of these people will agree with but I think that some of them would be fun to have in.
1. I know some might disagree this this one but reclaimable counties. So when the Aliens get a county on their side, you can get it back. I don't think this should be easy, I think it should be really hard but doable. What I was thinking was first you have to be so far in research for example, you have to have found about the microbes in the aliens and\or some other tech. Next you have to catch a alien and do research on him but only after the county has switched. Then you have so many days to do so many special mission in that county. If you fail at it than you have to start back with catching a new alien because the microbes adapted to your vaccine.
I know this would be lots of work to program. I also think that you could have it as a setting so you can turn it off to make the game harder.
2. I know one had been posted before or something like it, so don't sue me for it. Some weapons should be upgradeable mostly rockets and grenades. So you get rocket and rocket v2. And flash grenade and then stun grenade.
3. Most of the Alien stuff you can't research until you get a alien that can tell you how it works. Doing this will make it research slower and the game longer but will stop people jumping to the best weapon in the game. Like in X-com jumping from rifles to heavy plasma. Plus it will get you to think of ways to catch Aliens.
All of these are in just rough ideas.
The more people put there heads together the great the idea.