I don't really like how the independent faction works out, they fill a lot of roles of independent merchants, smugglers and bounty hunters which is all great but then they have their own planets and they don't really interact with other factions, so they don't really sound too independent.
It's also strange that with the other factions all pretty much geared up for war with anyone that they just decide to leave Independents alone. Do pirates even raid Independent worlds? (They probably do but I don't remember seeing it)
I think Independents shouldn't have planets or stations, they are just truly independent fleets that go about their business.
I think a player should lose or gain reputation with Independents based on their actions against all factions. Like if the player attacks a Tri-Tachyon merchant fleet while not being commissioned with a faction fighting Tri-Tachyon then they should lose lots of rep with Tri-Tach and a little bit of rep with Independents for unprovoked actions in the sector. Can gain rep by fighting pirates/pathers, maybe even [REDACTED].
Get a hostile enough reputation and then Independent bounty hunters start coming for you, gain good reputation and then you could get better missions or bar events. I was going to say maybe discount or access to goods in black market but then that sounds more shady, it already feels weird lumping in merchants, bounty hunters and smugglers together anyway, but I don't think they need to be separate factions.