The game certainly has inconsistent pacing, some of it comes from inherent problems in any genre where you get powerful over time.
For example the early game is, almost by definition, the hardest part. No matter how easy the start you pick, the game will almost always get easier from there as you acquire more resources and fleets, and if it doesn't, well it ends because you screwed up (or you just reload a save). Worse as it is right now the early game feels like a very heavy knowledge test, where the first few times you play it's just insanely hard as there's a lot to learn, but once you get it it's not that hard to abuse something to basically skip it.
Even if the pacing is slowed down (so each phase of the game feels more meaningful, rather than going from scraping by to planetary warlord) mid and end game can still certainly be an issue.
There's a few ways to add difficulty to a game like this:
1. Things like the spacer start (harder starting conditions).
Thoughts/issues- Mainly that it's only hard until you manage to get on even footing with another start (so a wolf + a Shepard + some pocket change). If you can manage to do that, congrats, you're now where you would've been had you picked that start from the first place, and are clearly skilled enough to win from there , because you just got to that point from somewhere worse, and the difficulty spike is over. The debt adds some longevity to it, but this is basically a challenge run that ends when you stablize.
2. Alternate playing conditions (like choosing a starting team in nex):
Thoughts/Issues- like the above, the conditions this starts you in only last until you get you way out of them, but I do think it's got the potential to help with replayability. Suppose you start as an outlaw with a pirate fleet, but major rep penalties across the factions, or a wanted rebel who can work with smaller factions but has an open bounty on them from the main ones, or a totally unarmed smuggler fleet? The upside here being that while you could just quickly do whatever is needed to pivot to "optimal" play, it also encourages trying something different.
3. Widening the power gap:
Thoughts/issues- right now I think it's still way too easy to get good ships. Ignoring blueprints, ships are decently cheap and salvage is huge. I still think ships should be locked up tighter and harder to find if you aren't part of the military, meaning you'd have to salvage or buy the larger ones. Salvage, since d mods are no longer such a huge downside, should be more rare unless you have skills and equipment to make it easier. Right now I can wind up being offered 1/4th of an enemy fleet, so in a few won battles I've got what they've got with any decent luck, but there's no skill involved besides "win". If salvage and restored hulls become harder to find, you can finally have a ship economy as well, rather than the current situation where even the rarest stuff sells for peanuts.
Oddly weapons are much harder to get reliably than ships, and are in a better place. I do think rare weapons should sell for and cost more though, thus making another reason to look into low vs high tech.
4. Escalating content:
The only real example of this right now is the redacted, and that's some of the issue. You go out exploring, find some hazards, kill what you can, and repeat until you know you're unbeatable. There's nothing really wrong with this except for the lack of options. There's one "boss" faction in the game, and then your other end game option is just going to war with everyone and fighting giant doom fleets.
This can be fun, but more variety would be nice (the 3 types of stations added , each with 3 levels really help). Maybe a few "elite" fleets that each faction can field which will only engage you when they REALLY hate you. 2+ for each faction, with each fleet showing off a different faction doctrine optimized to the extreme, maybe with a special ship/weapon (or maybe not, them playing fair is interesting too).
All that said the game is still pretty good as is. If it were just numbers tweaks from here I think you could still accomplish a lot to even out the gameplay (i'm a big believe in non RNG scarcity doing wonders for game feel).