Splitting up the independents into several factions is a very slippery slope, considering for example, bounty hunters could each have their own reason whether or not they'd go for a bounty on your head, eg. the bounty was put up by Pirates.
This is why I described a bounty hunters guild. All bounty hunters are not necessarily part of the guild, but the one who are have an agreed upon set of rules, such as staying independent of political conflicts, and not engaging in piracy. Lore wise it's not hard to justify. If you've played the escape velocity series, thats how they dealt with these things. It worked very well.
I really don't have a good answer myself. Everything I try to think of starts simple, and ends up a complicated mess. Because let's say you *** off the authorities on Independent planet A? Independent planet B is halfway across the populated sector, is a backwater shithole and can't afford to refuse the business you might bring, or might not even care in the first place. How do you emulate this without going down the route of making each independent planet and station its own faction? Is that necessarily a bad thing?
This is what I was talking about with the planet wise relationships. You kill an independent in that system.The independent stations in that system and maybe neighboring systems now are mad at you. As systems get farther away, the effect is lessened, so two or three systems away, they might only be suspicious, and on the other side of the sector, the effect might be minimal. You could also have an over-all relationship with the faction, which the planet-wise relationships would decay to over time.
A scenario that might play out is:
You start with a relationship of 50 with a faction on all planets and the overall faction.
You get into a fight with a patrol over a scan or something.
Your relationship in that system goes to hostile (I think it's -50).
The neighboring systems go to -40 or something like that.
Further out systems have less of a penalty, the furthest dropping to 0
Your overall faction is now the same as the relationship with the capital system of that faction, lets say that was -15 because it was fairly far away.
You then go to a different factions systems for a significant amount of time, when you come back, you relationship with all faction planets will have decayed to the overall faction relationship of -15.
You could simplify this by getting rid of overall relationship and just having planet-wise relationships. Some of the mechanics are already kinda in the game with the station commander relationships. This would be similar to making patrols and stations in a system behave based on your relationship with the station commander rather than the overall faction relationship.
It's certainly not simple but I think it's intuitive enough. Nearby planets hear about your actions more directly so their response is more pronounced, far off planets might only hear rumors so they don't react as strongly. You would definitely need a way in the map to indicate to a player what their relationship is with planet in each system is, could be an overlay or something. That UI could be tricky/messy.
The added benefit of this is that giving AI cores to a commander would not instantly improve your relationship with entire faction either. It feels more realistic in that way, your cores might get you into that port but not the whole faction. Giving cores to the capital would help a lot more than a tiny backwater, etc.
