Djinn, as in the creature from ancient Arabian mythology.

 I thought that the concept of a naturally formless, though sometimes manifest, otherworldly creatures that lead unseen but parallel lives to human societies, fits the stealthy wraithlike qualities of the new faction well. Additionally, Djinn are said to have existed before humans were created, in Islamic mythology, which fits the 'ancient alien' criteria as well. 

While I understand that the concept art given for the wraith choice is only illustrative not concrete; the suggestion of facial features in a nebular form conjured in my mind images of ghostly eyes and an ever shifting form, seen but unseen, that I imagine a Djinn might possess, glimpsed out of the corner of one's eye during a sandstorm while crossing the desert.

 The ambivalent moral character of Djinn, some djinn brought sickness and death while others assisted or ignored humans, would not conflict with however the lore evolves.   

Also, like sarin555's Species-0010 suggestion, the Djinn would be the name used by others (UE) to refere to the new faction, not what they call themselves. Their own name would remain a secret, to emphasize their obscure, shadowlike modus operandi.

Another thing, the current favorite species emblem has a resemblance to a simplified Arabic calligraphic art.