Templar and Omar wouldn't make any sense in my opinion since they would either abolish all biomods or eliminate the other factions, and hardly believe they're going to base their game on the Omar
So that leaves Apostlecorp and Illuminati. I voted Apostlecorp, then realized however that that would set the game among the borg-esque dominance of Denton and Helios. The Illuminati ending would be the most fitting, but the Dentons would be dead.
So, in the end, I can't really decide, but I look forward to the game!