The real good guys are the independents. You never hear them starting wars, blockading colonies or stealing AI cores. They just chill. They're like the capybaras of the Persean sector because you have to purposely go out of your way to make them angry.
Independents really do a number on the League's place in the narrative. If some number of these independent planets relied on the League to reinforce their independence (e.g. if the Church were after Baetis for the same reason it comes after the player), and the Hegemony really were expansionist, they'd make a lot more sense.
As it is, it feels like they're tilting at windmills. The Hegemony, at this point, doesn't even care if you're operating a drug den right outside its borders. They're too reasonable and noninterventionist for a faction whose sole purpose is 'defying' them to justify itself.
I get why Independents are implemented the way that they are, but having some/most of the game's independent markets under their umbrella would do a much better job of humanizing them while also paring down the questions that are raised by every single scavenger, explorer, and mercenary fleet being in a military alliance with Nortia and Derinkuyu Mining Station.
Within Hegemony space:*
Nomios and its cryo facilities being in Hegemony space while also being open to everyone makes them feel really weird as a faction, especially in conjunction with Galatia. They're way more kumbaya about these things than you'd expect them to be - moreso even than any real-world nation would be, even ones that are much more laissez faire.
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Agreus is a bit odd, given that it's also in Hegemony space and has very little keeping it independent. I'm not sure how I could justify this, honestly - unless the Hegemony are explicitly "the good guys", there's no way they'd tolerate a full factory complex outside of their economic and political control in their space when it's dependent on them for service anyways. Is there a reason they can't just be a Hegemony market known for independent sentiments?
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Nortia is technically in Diktat space, but they're written as a Hegemony client state of Askonian rebels. I get nobody being at the helm, but it's still odd that the Diktat hasn't crushed them, given that they're (ostensibly) their explicit enemies, and they've had years to fly over, break the defenders, and perform a tactical bombardment on the place, then just decommission all of the industry and bring it back home as scrap to sift through.
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Asharu has very little in terms of leverage, but is in a very Hegemony-controlled system. Given that the Hegemony has a lot of people to feed, it seems unlikely that they'd just let a food exporter stick around outside of their control..
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Derinkuyu is independent, for reasons I'm not really sure of. Given that they hosted pirates, I would think that the Hegemony would come in and clear that up, perhaps forcefully. Given that most of the tutorial presents the Hegemony in a very heroic light, having the reintegration of Derinkuyu occur after the player leaves might add depth to the opening scene.
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Orthrus is a mining world in Hegemony territory that supplies the fuel production facilities on Sphinx. Again, even if the Hegemony were the nicest, friendliest, most perfect polity on Earth, there's no way they'd let it be independent in any meaningful way.
Overall, it seems very strange that, while League-local independent markets all have text relating to how they escaped League control, Hegemony-local independent markets are apparently under no pressure to start paying taxes. I'd add some lines indicating tension with Nomios, and maybe an interaction or two in which the Hegemony intermittently blockades them. They're a nerve center for the sector's rich and powerful, located well within the Hegemony's grasp. I'd make Agreus and Asharu Hegemony markets, and add a line or two about their plucky independent polities gradually being brought to heel by the prevailing winds of the sector (in Agreus's case) or their dire situations being used to justify the appointment of a Hegemony governor (in Asharu's case). Orthrus, given its critical resource and its strategic location, could be said to have been taken over quickly and without any heed to local objections by Hegemony military forces early on in post-collapse history. Likewise, I think Nortia would be more plausible and more interesting if it were explicitly Hegemony-flagged, with some text about the rebels not especially liking the arrangement but recognizing that they don't have any other options. Derinkuyu could be a Hegemony market, with some text about British Navy - style treatment of the locals who turned pirate, even if they had no other options, or the hanging of a few examples while the rest remained as miners to keep the system's economy stable - but were forbidden to leave the station.
Within League space:*
Ilm is effectively a subsidiary of Mazalot, taking in workers and sending home remittances. It could use a better justification for remaining independent, given that it's League-dependent and in a League system.
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Ailmar is portrayed as making deals with other factions to stay out of the local kingdom (and the League). That seems a little too easy, IMO, given what they put the player through. Maybe it'd make more sense to base their independence around the local "kingdom" not
wanting to admit them into the League, preferring to deal with them from within the protection of a larger polity while leaving them without it, and at a disadvantage when writing trade deals.
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Eldfell is independent, but explicitly stated to be run by economic power-players on Kazeron. It's a bit strange that Kazeron would let it get out of paying taxes and not act to secure it, given that it contains their refining facilities (instead of those being on Kazeron, for some reason).
These planets could be left independent, as a sort of demonstration that the League, while somewhat expansionist, is willing to let individual markets go without paying taxes as long as they aren't a major threat, don't cause any problems, and would be a hassle to integrate. It'd give some small amount of merit to their claims of supporting planetary self-determination. Maybe add something to their descriptions about appealing to the League for independence, and that appeal being granted - perhaps to keep up appearances, and perhaps because they have nothing worth taking. Alternatively, some kind of League guideline around permitting and guaranteeing independent colonies as a gesture of goodwill could be offered as an explanation for their existence, with Eldfell's local refining monopoly being a part of that outreach.
Other:*
Nova Maxios is the headquarters of the sector's independents. Right now, they've got a story about being plucky underdogs who make it despite the Powers that Be, but nothing really comes to cause trouble for them. Given that they're next to Kanta's Den and a Tri-Tach market, some kind of shady deals could be mentioned in reference to them. Alternatively, they could just be a League market - the League could use one or two success stories, given that almost all of their markets' narratives focus primarily on how awful they are. A working industrial complex with a nanoforge would be a prime target for the Hegemony or Tri-Tachyon, not to mention the nearby pirates. I think their story would be tied up very neatly if those things had caused problems for them in the past, leading their government to officially request League integration and receive military support as a result, almost operating as a mascot for the Persean League (with the rule exceptions and favoritism that entails) due to the very marketable story it lets them tell.
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Baetis, as mentioned, could just be a Church market, with the flavor text indicating that its authorities permit a bit more latitude than other Church worlds, but keeping close watch on the individuals that make use of the extra freedom. To help add a sense of ongoing history, it could formerly have been an independent world, before the Church imposed itself on the local authorities (with some covert assistance from the Luddic Path).
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Cethlenn is a money laundering site for Tri-Tachyon, which fits the faction's profile fairly well and emphasizes that Tri-Tach is a force for laissez faire governance in the sector, if only because oppression is expensive and yields no immediate income. Makes sense to leave it independent.
Overall, I think the independent markets would be more interesting allocated like this:
Nomios, size 3, Arcadia Star System (Independent; contested)
Agreus, size 5, Arcadia Star System (Hegemony)
Nortia, size 4, Askonia Star System (Hegemony)
Asharu, size 4, Corvus Star System (Hegemony)
Baetis, size 5, Eos Exodus Star System (Luddic Church)
Derinkuyu Mining Station, size 4, Galatia Star System (Hegemony)
Cethlenn, size 4, Hybrasil Star System (Independent)
Nova Maxios, size 4, Magec Star System (League)
Orthrus, size 4, Samarra Star System (Hegemony)
Eldfell, size 5, Thule Star System (Independent)
Ailmar, size 5, Westernesse Star System (Independent)
Ilm, size 5, Zagan Star System (Independent)
Instead of a bunch of rabble-rousers that are inexplicably perfectly coordinated, universally beloved by spacers, and tolerated by everyone in power, market affiliation with the Independents would be restricted to interests with either a very strong claim to it or a powerful patron faction with a good reason to forego power projection and tax revenue and back their independence.