It would very interesting if you made it so we could play as of the minor factions.  Each starting off with a added bonus being that they are smaller than the major factions, and each having a very unique game-play experience.  For example, you could make it so Pilgrims start off with a nomadic fleet and focus on finding the Endless home-world rather than traditional objectives, and only be able to have temporary settlements until they do, once they find it, they can colonize it and it becomes their home-world, as well as allowing them to take control of all planets they have previously settled on.  These experiences would vary from faction to faction.