The thing is is that aliens are, well, alien. It is hard to make them "real" at all without them looking a bit silly. Heck, even in fantasy games I tend to stick with playing humans.
I much prefer the aliens to be the new, scary badguys that have just been encountered and have to be dealt with. Y'know the characters just hate it when they go to deal with these space pirates and they turn out to be an alien advance-guard/scouting unit, that is just out gathering info on these "humans" so they can learn to defeat them.
Of course, the ultimate culmination of the story could be not to fight and defeat them, but to learn to co-exist with them, that we have things in common. [Like it could go the way of Enemy Mine, which is a great movie.]
But, for the most part, the characters are all humans (or transhumans, alterant replicants, etc.....).