I'm an amateur game designer (free time, bored, etc.), and this seems likes the beginning of a great game. I suggest unlocking different move or effectiveness of existing moves somehow. A will wait for a sequel and take as long as you want, having to switch to another program might be needed for upgrades.
A reload feature might add to the skill requirement of this game. Like clip sizes. Otherwise I can just shoot my pistol nonstop, not needing much else.
Try using the cloak on the alien capture the flag missions, saved me a lot of time. Aslo the holy grail sniper in my opinion is the best weapon. +1 to keep alive