I remember Zantai talked about the faction system in one of the streams and how they didn’t really get too far with it. I don’t think the system needs very much to feel better but I have an idea that may have been mentioned before.
Some games with reputation systems reward players with supply chests or other things after gaining x amount of rep after reaching the rep cap and I think it would fit nicely here as well. The rewards don’t have to be too crazy, just a small supply crate or something else every time you reach a certain amount of rep with a faction would feel nice. It would make the system feel just a bit more fleshed out and you would no longer see the extra rep gained as a “wasted resource” (I don’t know if others feel that way, but I think about it sometimes).
I don’t know how much work this would require to implement, but it may be the one thing you could do without focusing your work too hard on factions 