Yeah, early game will definitely be easier. But the moment you leave the starting system/tutorial you're still at the hardest part of the game, with every thing after getting progressively easier until you're unstoppable. Which, in a general sense, is OK, I think.
Personally I think the issue is not only that the early game is difficult but also that the later game is trivial and far less interesting.
Agreed. A solid solution to that are high-difficulty areas, but that's not straightforward in Starsector. After all, high level enemies are self-made, by going to war with a faction. As long as you don't do that you can go everywhere.
Maybe it would help if factions would establish patrolled no-go zones, where you are attacked on sight. Could be entire systems. I imagine there would be all kind of nice hardware and secrets to discover in these zones, if you manage to fight your way through (or get exclusively allied with the faction). At the moment there's just no real external motivation to start fights with the strong factions.
A high level general baddy would also be good, some kinda super pirates. Rough AIs or some such, hopefully story related.