I think it d0epends on what kind of game it is: in Ufo games the aliens are always the scary ones, while the people who kill the aliens are brave, courageous and noble... "Dulce et decorum est pro patria mori"
On the other hand, in an apocaliptic, psykolacal or horror piece, the Super-humen are going to be just as bad and cruel as their enemies. Or even worse, becouse they are humans, and humans are so much inperfect.