One thing that strikes me as interesting while I'm playing starsector with nex is the RP aspect of it. Like you said, you haven't stepped too far away from the fleet mechanics, because that is the core gameplay. However, in many ways, starsector is also a text-based roleplaying adventure game (which apparently we'll be seeing more of in the next update) and as such, you are ONE person. No matter what you tell yourself is actually happening when you set up a new faction, you're basically a dictator. You enforce strict policies which decide what is or is not built on your colonies and those decrees are enforced. Not only this, but unlike other 4X games where you sometimes feel like even though I'm technically an immortal Xerxes or Napoleon or the hand of god influencing the Bug Hive mind, in Starsector, you are explicitly one human (or Ai core, depending on your portrait). When you start the game, you type in your name and choose your appearance. You're one person and there's no changing that. So whatever direction this mod goes, the more it leans into that fact, the better it'll be.
What follows is speculation and wishful thinking of a type of game I would enjoy, purely an example of a design direction that I think would work, not a suggestion.
To take agents, for example. What if the player could bring an agent along with the fleet to ease restrictions into and out of certain ports or factions (like some sort of abstract version of an Inara character), especially if there was more dialogue/rules involved with docking and mining and transportation and contraband and so on. This would be especially interesting if administration/colonizing was much slower/more expensive so that only extremely rich and well connected (read: friendly with powerful factions) commanders could pull it off. In other words, turning colonization itself into the lategame goal (by making it much much harder) and turning the acquisition of a powerful fleet/influence into the main midgame goal. Maybe you settle some tiny mining colony on some moon or re-populate some lost astropolis into a freeport (just not freeport 7 lol rip) before acquiring an actual full-fledged colony. There would be a lot of features and tweaking that would help flesh this out, such as growth rates based on immigration, immigration being tracked, a more robust economy system, a much more robust reputation system (with differences between Faction reputation (how much they like you), Faction standing (current official political climate), market reputation (the Jangala officials are going to hate you if you sell tons of opium there, even if hegemony likes you), and many more.
Obviously this fantasy of where starsector, nex (and I guess maybe terraforming) go in the future is just that, a fantasy. But rest assured that the more the core gameplay loops (system exploration and fleet-based combat) are leaned into and supported, the better this experience will be. Also rest assured that I have the highest hopes for this mod and this game. It's pretty great and you should feel great about it.
P.S. there's also trading and mining, I guess, but those barely register when compared to exploration and combat. Mining in particular seems very off right now, very much not the point of this game. (unlike in games like freelancer where it was a (sometimes) boring, if extremely profitable way to play. I still remember mining diamonds on the edge of an uncivilized system, dodging red hessian patrols and wishing I was in Kusari space with its beautiful vistas, but that was so far, and I needed to make a buck.)
edit: can an agent have multiple tags?