I think there's an inherent problem with having factions for supposedly factionless people, and this goes both for Independent as well as Pirates. I know it's like this because the alternative is probably a hell of a lot of work. If you've played STALKER's CoC mod with dynamic relations, it's the same issue. These "factions" are each comprised of people doing their own thing, each concentrating on their own survival and gain, over any wide-ranging strategic or ideological goals - and if any have such goals, they aren't necessarily shared with other members of the "faction". They aren't organised in the same way as the Hegemony or Tri-Tachyon. A bounty hunter going after pirates for the hegemony isn't going to share the same interests as a smuggler - Which is another thing that bugs me. These smuggler fleets shouldn't be designated as such, they should only really be identifiable by their behaviour (Transponder off/going dark on approach) and fleet composition. But their very existence is pointless gameplay wise, since you're going to *** off that entire "faction" for engaging them despite that fleet's criminal acts, while the system's authority might reasonably see such an action as lawful. There's more aspects and facets to this issue, but I don't really have a solution other than making each independent world, and each independent fleet type their own sub-faction. If you rack up a bounty, all the bounty hunters will be hostile to you (With some actively hunting you). If you're constantly pirating independent trade fleets, they'll spread word to one another and put that bounty on your head, while avoiding your fleet themselves. If you're targeting smugglers, those other sub-factions shouldn't care.
most games like this you cant avoid the consequences of your actions. it becomes too easy for the player.
I think it simply makes sense that if a fleet is outside communication range of the civilised systems, they shouldn't be able to communicate they were attacked by you or any others. In such a situation, what consequence would there actually be? As the economy systems become more complex, this could be a viable means to create instability, or on the other hand, the player (and AI fleets) could take jobs to escort scavenger fleets.