I honestly think there's a glaring problem here -
This either needs to be scaled depending on player count, or needs a 'minimum' amount of players before a round begins to make sure it's not just a one man army or whatever.
Also, could there be NPC's beside civs/aliens, such as a soldier NPC or a police NPC, or a criminal?
As a final suggestion: there should be an X-Com-esque team/unit/whatever that's basically an elite version of soldiers. They'd have a random strong gun(chosen by the minigame's setup), a grenade of some sort, a healing kit, and a strong melee weapon. There'd be roughly six people on this team, including a 'leader' of sorts who basically decides what the team would do. They'd all have 3/4ths max ammo except for the leader, who would have a full set of ammunition and two strong guns(also chosen by the minigame setup).