I think the main thing is that OP doesn't enjoy combat. The game is at its core a good combat sim. Everything else was added later. If you don't enjoy that part of the game, you're left with a much thinner experience. And even if you do enjoy the combat, the game has a definite arc where progress beyond some point carries less and less meaning.
I do enjoy combat, just not as much as exploration. When the game presents a strong enough argument for it, it's really good and fun (well, unless the AI screws you over). The game doesn't do it often enough for me, unfortunately. Most battles seem optional, like ghost vaults or teleporter rooms in DCSS, but those - which I generally pounce on, or at least consider very seriously - always come with a promise of Good Stuff should I meet the challenge. It's very easy to avoid fights - heck, apparently I've been dodging perma-hostile scavengers without realizing it all this time - and not a whole lot of in-game reasons not to. This is subjective, of course: what's one person's easy bounty money is another's "nope, I'm gonna die", and I'm closer to the "I'm gonna die" end of the spectrum. Improving myself would be a solution, but it requires motivation, and the game should ideally provide it. Touhou keeps me going by having a really short replay cycle, DCSS - by the virtue of RNG-caused failures happening mostly early on and the rest being my own fault and easy to analyze. I can't say for sure what would keep me going after harder fights in Starsector. Ruthless Sector is very close with its take on battle difficulty, it's quite fun to strike the balance between XP bonus and my skill level and it does nudge me often enough to deploy less ships and pilot better.
The only thing I would call a satisfactory extension to this without being predictable would be attempts to improve the emergent storytelling of the game; that is, a network of events and AI that produce a continuing shift in story politically, financially, militarily that involves the player. All other endgame additions are just staying the inevitable "Game Over". Crusader Kings accomplishes this by its The Sims: Medieval Bloodlines take on storytelling, for example. Or Dwarf Fortress which is by its nature a fantasy storytelling sim that goes into great detail. This is probably not the intended trajectory for SS though. As much as I would like to see dynamic power politics in the game.
This would be wonderful. The most memorable and fun fight I've had was like this: a Nex invasion fleet I absolutely had to defeat. A natural outcome of current state of the game world, with ample time to prepare, challenging with great rewards and big stakes. Nex's invasions make for great boss battles tbh. It doesn't have to be done the Nex/4X way, either - I have a feeling that contacts have a great potential for making the world more alive. They currently don't make any long intricate stories because they don't (to the best of my knowledge) interact with each other and exist just to be quest givers.
The problem is that Alex has clearly stated that he doesn't want Nex to be part of the base game, not even as AI battling each other for supremacy.
So yeah, "dynamic power politics" is gone down the drain.
I honestly think this is the biggest mistake Alex is making. Imagine if after our first one or two colony, we could have our faction just colonize themselves (and the current factions doing it themselves as well) and then because of territorial disputes and other issues, wars would arise without the player necessarily having a go at it, now I haven't played in a while so I don't know what Nex is capable of but from what I remember it was a pretty passive mod with the player having to start the mega wars.
We'd have to make resources like fuel, supplies, weapons, hulls, food, etc more meaningful and less planets would be viable for colonization just for that purpose (to limit resources that can be had overall) so you'd have to actually engage if you don't want to "lose".
I think in this case enacting a colony should just make it so that you enter a state of the game where if you lose your faction, you lose the game.
Obviously, the end game is supremacy, what else could it be? But even this can tie into something bigger since the factions themselves are remnants after the gates have closed off, so unifying the whole thing to then engage into different questlines explaining the situation in the "universe".
From there you can basically do anything storywise but at least gameplay is a whole lot more meaningful in terms of combat, immersion and the world being "alive", you know?
Since I'm not a guy that is into "exploration", I don't have any ideas for that, but I'm sure my "suggestion" (just Nex++ basically) is pretty open-ended and allows a lot of freedom.