I very much doubt that'll be the case. For starters, the devs (Will Miller in particular) have said Beyond Earth, and Civilization in general, is very much about the story of humanity. In addition, alien factions would have to be completely different from human ones, from cities to buildings to units. And they wouldn't really be compatible with the Affinities system, possibly not even Virtues. Overall, they don't fit. Just slapping on aliens which are functionally 95% the same as humans would be cheap and frankly terrible. And giving their implementation the depth it deserves would require even more than a full expansion.