In other games, power and difficulty typically progresses either with time (e.g. if you waste time in Starcraft, your opponent might take the initiative - but you also get more and different units) or with distance covered, areas unlocked or other kind of moving from one place to another (e.g. as you travel the world in Ori and the Blind Forest to find new abilities, but you also encounter more and tougher enemies).
I think I would prefer Starsector to get more difficult with time, since it leaves more freedom about getting to the final goal. One thing is, say, defeating hypershunt guardians, but another is doing it in the timespan of, idk, 5 years. Right now, you can explore and trade for years, then just throw bodies at them, once you get bored of doing other things.
That said, I think I would prefer some more interactive system, like a faction expanding to eventually kill everything with some singular weak point, with the player either rushing the objective before too many enemy forces are present, going after weaker fleets of that faction for loot and to impede the progress, or getting money from trade to afford the ultimate fleet and have a big old fleet fight at the end.
