I was thinking it would maybe be more interesting to introduce an injury and insanity system for the soldiers, as the constant missions wears them down. So as they become more powerful but also develop weaknesses too and perhaps become useless. At the moment a lot of the game seems without consequence and injuries seem like one of those things. At the extreme end you could have soldiers losing limbs and needing prosthetic replacements (improved by either mutation or cybernetics) or maybe becoming trigger happy or cowardly as the psychological damage/effects of fighting an alien enemy.
Anyways, just a passing idea, I think the development of the game is going well and I think it’ll be really good when its finished.