Still very limited on missions. I get like maybe 3 missions, the rest says they dont trust me enough. Yes I am friendly with the sub-faction as well. Also I thought the better the rep = better rewards from missions?
I think the game dumps a set of missions randomly but has a percentage to give the higher up missions. I think population/economic condition may also affect your missions.
This is all assumption based on my experiences. Don't take it for fact. ^^'
I´m close before giving up on Feds, I´m unfriendly to them since 3 weeks now, failed only one mission for them so far since I try to fix the rep, befriended/allied several sub-factions and these punks still dont like me.