I like what Traceur said about beasts and gods - the chances of an alien species being at a comparable level of sentience to us is small. That said, this is a game, not reality, and game design should follow what is fun and engaging, not what is merely probable. My preference would be for there to be no advanced aliens that still exist, but as we build star-gates and travel to other systems we start to uncover the crumbling remains of other star-faring civilizations, leaving us a mystery as to what happened to them and why none are still around. Is advanced civilization inherently unstable? Is there something out there killing off advanced civs? The archaeological remains would provide aesthetic interest, as well as the shells of bases that could be repaired, and of course derelict alien tech that could potentially be reverse engineered.