Troops Units can make a nuisance of themselves, particularly by the time you reach the final battle, but you can prevent the game from sending them your way as frequently with a bit of preparation. In the first two or three missions, avoid taking out any enemy ships except those that send fireballs toward your structures. Instead, tend to the Troop Units that come at you. Keep doing that and by the time you finish the third mission or so, you should notice that you're facing barely any Troop Units at all. This condition will persist through the remainder of the game, even if you have to continue from time to time, and it will make the later battles much easier to take.