I see a potential link with the non-Human player. While I dislike the idea of not playing as Human (because all the asymmetry and lore around that), I like the idea of different openings. Choosing one unlockable ship is a start, but it sure can be more complex and interesting. And about the non-Human opening, I could see things like MF allied from the start: a Spire battalion, some friendly Roaming Enclaves, one Zenith Golem, some Resistance Fighters... Might require something for the AI to balance, or let the player put nasty plots.
Technically, my ideas sound like good-only Minor Factions (which might be a good idea). Eh, AI Types already sounds like plots to me. I bet something more smooth and unified will evens everything. (In the end, only the lore makes a difference... and the hostile/friendly distinction, of course.)