what about a combination of xenonauts with total war, world in conflict or war game: European escalation and adding some elements from 4X games like sin of a solar empire (like the ability to design u own weapons)?
the story could be something like that we discovered that the xenonauts where fighting all this time against a supply fleet who went the wrong way and the fleet commander thought it could became more powerful or get up on the ranks by conquering ours planet. so after no hearing in a long time from this fleet they aliens send a recon fleet to investigate what happened they discover a transmission requesting for help and decide to bring the big.... big.... big.....BIG..... did im already say bigs....guns and send a more battle experienced fleet to conquest us.
so like in xenonauts u now need now to protect earth by controlling all the world military against the alien menace but now u can control entires platoon of troops, tanks and arties along with being able of calling air support from helos and planes which the aliens can do too. u now have to no only repel alien landings but also fight for air superiority in most of u country (and in the landings,crash and terror missions zones if u wish to have air support or to prevent the aliens for having it) by fighting their squadrons of fighters and capital ships with u owns fighters and u own reversed engineered capital ships ( or we could have the naval fleets of that time modified with better armor and weapons and FLOAT DEVICES!!!!!! ) launched by bases on u countries.
u could have one or various persistent army/battalion spread in different bases on the world. u could be able to personalized u platoons by editing their load out and something similar to the vehicles they could also have some kind of stats system where they get better in some specified stats depending of what they did on the missions or the usual experience system where they get better with every battle they fight . u could also be able to design u own vehicles by being able to choose between different hulls and choose which equipment, weapons, armor, transmission and all that stuff, every election having it advantages and disadvantage.
the missions could be the usual but BIGGER S!!!! and adding things like alternative objectives like in a terror mission u could win by either killing/repelling all the aliens or capturing/destroying the aliens carriers ships while they are on the ground. with also be able to request bombardments on missions sites, intelligence missions, special forces strikes and Tactical nuclears attacks to soften up them.