Title. I think that having each market as an entity independent from their faction (but still a part of said faction) would be a much more immersive choice to simulating the political chaos of the Sector prior to the Collapse. A lot of planets that are independents or pirates don't share much in common, their needs, wants, and collective motivations different from each other, and I think it would be interesting if, say, you could fund and support the Askonian Revolutionary Council on Umbra and use it as a base to attack the Sindrian Diktat; Or convince a few of the Persean League member worlds such as Olinadu to leave and join your faction, either through promises of investment and economic growth, or coercing them through the threat of an imminent "cleansing" and "salvation" of AM fuel bombs.
I don't know how exactly it would look, but I would imagine that each world/market has priorties it wants to accomplish, and will take different measures to ensure those goals are met, whether it be growing their economies and market shares or seeking security. A market seeking drugs or organs might divert their patrols or distract them in order to let you in to trade and provide their markets with the necessary goods. You could do this by getting in touch with colony leaders via the comm net and offer discounted (but still profitable for you) prices for needed goods on the condition that they tell their patrols to stand down, even if the faction they're a part of is hostile towards you, and depending on their allegiance to that faction. Hegemony colonies will likely not accept such a deal unless they're really desperate, while independent and pirate colonies will be more agreeable to such a deal since they are such loosely allied with their respective factions. A pirate world with a surplus of underpaid miners or mercenaries may be convinced to ally with you if you offer them a job raiding and conquering worlds or offer to eliminate any market competition, either for access to their markets or for a price of credits or ships.
This would also allow the factions to place lower or higher priority on which worlds and systems it wants to protect. For instance, Asharu (in the Corvus system) is a world with only a lingering amount of economic activity and importance, so independents generally shouldn't care if it's invaded as their relative market share is too insigificant to justify getting mad at you or any other faction. Independents are, as stated in the faction description in-game, as likely to cooperate with each other as they are to look away from their neighbors' misfortunes.
I would also like to suggest that colonies be subject to politics as well. Maybe in the first stages of setting up a colony (around size 3 or 4), the population will generally listen to you and accept your autocratic rule. Think about it; in-game the player gets all the income from their colonies of potentially millions of people all for themselves, and they decide what to do with them. This is, from a story and lore perspective, what I believe makes colonies so overpowered, and makes the player able to completely uproot the status quo of 200 years of chaos in the Sector in just a decade or less. The millions of people who are funding you and you alone are just too accepting of your rule, and I think that adding some sort of government that you can partake in, elect or control would balance the dynamic out.
Autocracies and dictatorships will require many resources funneled into keeping the population in line and keeping them happy enough so that they don't revolt. This will give you the greatest share of income from your colonies, but you will semi-regularly have to put down rebellions and funnel a significant amount of money into your military and patrol forces. It will also make other factions less likely to trade with you, unless the other faction has common interests or is also a dictatorship that has warmed up to you. Democracies, federations, and other forms of government will also be available, albeit giving you a smaller portion of your colony's income, and subject to having you compete with and cooperate with computer-generated representatives and candidates in your government. You can lobby them and retain control of your government, but whistleblowers might uncover your actions and reduce your colony's stability. If you manage your political situation really poorly in an attempt to exert control, you could trigger a full-blown revolt of the colonies you worked so hard to create.
Ultimately the goal here is to create a tug-of-war between you, your colonies, and the other factions and the polities that make them up. That's my whole spiel that I spent at least an hour writing from my thoughts, and I think it'd add new life into the Sector and give it a unique touch that you wouldn't get from any other space strategy sim on the market today. Bring the sector under the control of your benevolent democratic multi-planet federation or attempt the iron-fisted approach as the Hegemony and the Diktat have, and succeed in bringing the Sector under your personal rule and declare your domain an empire. I just needed to write this down before I forgot, and I hope the devs or some modders at least consider my thoughts, even if they won't be implemented in any way.
Have a good one