Some projects are big enough as modding that you might be better off making your own game rather than put that much work into a mod. This is probably the reason that those really ambitious mods that totally remake a game don't happen more often.
If you want a great character system in Starsector you'd have to design and build that from scratch, balance it, test it, debug it, and you're inevitably going to get people complaining at you for ongoing support for something you made for free, which is pretty much guaranteed since Starsector is a moving target. Plus, you have inter-mod compatibility to keep in mind, and people are going to get upset at you about that, too.
So at that point, just make your own game built around a character-centric engine, rather than shoehorning it on top of something else. There are many points I'd work on if doing that, but one of them is the concept of a faction owning something. In games, often things are just labeled as being owned or part of a faction, but in real life ... the concept of ownership only makes sense as a social contract between individuals. So, imagine if two mining companies both believe they have been granted rights to mine a specific asteroid, but those rights have been granted by either different factions, or different governmental departments who's jurisdictions overlap in some way. You could have some really complicated types of stories this way. I really like the idea of "procedural bureaucracy" leading to conflict, and it would be deeper than the normal way that's done where you just make a faction, then divide that up into territories, call those provinces or something, then proceduraly generate the details about each province.
Or you get things where when a faction's last city or planet falls, the faction "fades into history". The issue here is that the game engine is built around the "truth" that a specific faction owns a city or planet. So this doesn't allow for more complex stories to emerge naturally, such as a government in exile plotting to retake their home planet, or similar. Because of this kind of thing, merely tacking a character system on top of a given faction system may not allow as many organic types of stories to unfold.
I'd like to try making something where factions merely exist in people's minds, rather than being hard-coded as truths in the game engine.