This seems like a very inappropriate time to have this discussion.
For one, you can't get Firaxis to change anything before release. They were too far committed to the game's design even before they even announced it existed. The best you can hope for is alien factions in an expansion pack.
Secondly, the devs have alluded to a sort of open-form story told through quests. We don't really have a grasp on what that story is. Some reviewers have mentioned that it has to do with the Great Mistake. Others, that it is about the progenitor aliens. It's quite possible that the story would only make sense for Earth-origin factions.
Thirdly, The Contact Victory wouldn't make a bit of sense if you are already a sapient alien culture or if there are sapient aliens competing with you, because the point of it is to contact sapient aliens.
To want alien factions is to want a different game than Beyond Earth, because Beyond Earth is a game that is intrinsically about the human experience as an interstellar species. There is no counterpoint as it stands, and they can't put one into the game and still ship it on Oct. 24th. The alien point of view could very well serve as the foundation for an expansion pack, but you aren't going to get it now.