OK, been thinking about this for some time, and hence people keep making suggestions I will put my own.
1- Consistency of bases -Since ever the lack of consistency in the bases have nagged me (for example, going into a Bounty Hunters base to find Blood Dragons at the bar, and maybe (not the case) Weapons from Bretonia. The same go to some of the rumours that are geographically misplaced. I understand that this is a really methodical issue to fix taking more time than OP may have available, but it would really help with game immersion.
2- Reputation Consistency - Hence there isn't that many players to conduct role play, I would vote not to have clean reps, or, to have licenses to force a character into a faction. Of course a Junkers or Zoners licence would give you access to nearly everywhere, but maybe not to buy every single item (and maybe a faction hostile to Zoners could be created).
3-Pods could be differentiated by Faction, and have prices accordingly.
Maybe I am complicating to much and people just like the Arcade feeling, but I do think these would improve gameplay (Yes, maybe I am getting bored).
PS: We still don't really have a trade route that make's the journey to Altair worthy,