Something that really hasn’t been touched on in a proper action movie is stress due to violence. I don’t mean some bitch movie all about dealing with shellshock after the main character came home. I mean the guys from X-com could have night terrors, some wake up screaming (it becomes worse over the course of the movie) and none of them talk about it. One of the guys may see a kid he found in a building and was escorting to safety killed in front of him. He could have an arc where he’s never quite levelheaded around that type of alien afterwards. One time he freezes while his squadmates shoot. Another time he goes off and empties his clip at full auto. His story arch would be finding the internal strength to get it together and keep his cool knowing they’re going in to kill a whole group of these dudes. 
You could also deal with sacrifice. Not surprise last-minute I’ll-blow-everything-up sacrifice or “it’s a suicide mission” but they all survive. The whole movie could be an ensemble piece. One of the squads we follow could be sent on what they know is a suicide mission to gather intel. They all make their peace and go in grimly, fighting to the last man, getting as far in as they can while they’re shredded. 

There could also be moral ambiguity. We could see the same gruff commander we’ve grown to like over the course of the movie send in a wetworks team to kill townsfolks, women and children all, b/c some of the town’s known to be under alien control. It may bite them in the ass as a escapee of the attack who witnesses it from a hill-top believes the aliens are some work of the government they’re trying to keep under wraps. This leads to human attacks on x-com’s base that’re woefully underpowered. Yet the morality flips again when the medically examined survivor turns out to’ve been filled with such a zealous hatred of x-com b/c of partial alien control.