My vote is Imperium first, Kafer second, Galactic Empire third.
Imperium-(chance of uniting humanity: high) An ancient, vast, powerful, yet stagnant and corrupt empire that seeks to totally annihilate all Xenos. A empire that has vast fleets at its disposal, with large numbers of strong warships. Some of those warships are highly advanced, beyond anything humanity has ever seen, at or beyond the limit of current theory, yet the retrograde empire is no longer able to produce, or even in some cases maintain or supply the somewhat small number of these ancient vessels. Ditto ground forces. I'm guessing the economy aspects of the empire be nominally vast, but inefficient and nearly crippled by the weight of maintaining the ever increasing burden of the empire.
Kafer- (chance of uniting humanity: high) I don't know much about the setting, but I vote for it second because it looks like it would be unique, and seems to be a fairly popular choice. Any threat that is hellbent on destroying humanity is always going to be interesting and highly entertaining.
Galactic Empire- (chance of uniting humanity: medium) I imagine they would be stronger than any single human faction, but not the whole. They would be a bit more advanced than humanity, and would have the advantage of a strong, centralized government, military, and economy. Humanity would have its hands full with this threat. I'm not sure if you would give this faction internal problems, perhaps some rebel alliance that humanity could link up with. Of course, a rebel alliance could allow for a stronger Empire, and a more interesting war. (Empire mauls humanity, takes large losses, rebellion starts, forcing the Empire to shift its focus. Humanity gets breathing space, and doubles down on defeating the Empire.)
Just some of my thoughts on what these, "endgame" threats could be.