Let's see... I like the idea of taking the fight to aliens. Let's imagine that earth wasn't the only planet they tried the biomass project on (it would be stupid anyway), so there is another planet where allied human/grey forces fly to and try to clear the biomass through orbital bombardment. Their ship is shot down and crash lands. Now is where player comes in...using limited resources you have to call for help and hold off your position, in time you'd get reinforcements via small undetectable ships or just try to salvage and rescue crews of other ships. That's it for the story, now for game additions:
1) More mission types and working missions like biomass clearing (imagine squad of heavy armored soldiers burning everything down with heavy flamers) or sabotage ones (we could use some silenced weapons).
2) More normal (not bio) technology from human-grey cooperation.
3) Mechanical units (like robots or scouting/sabotagin devices) sound nice, also some extra implants maybe (easy to implement as additional training but you could only install limited number of those), and those would be needed anyway because of very limited human resources.
4) Automated sentry guns, mines and proximity grenades. Also making inc ammunition burn out the terrain and making flames burn longer in overall.
5) Calling in 1-2 airstrikes in open terrain mission (probably limited by aviable ships or ammo)
6) Power armors (heavy ones are just too weak in term of protection)
7) Close combat weapons (I find it silly to see greys firing rocket launchers and damaging interiors of their own ships)
More to come...