Created this account just to say this is genuinely dissappointing.
I strongly beleive you should be working towards making the game much more open ended by adding lots of scaling. The whole idea of starting new runs over and over will ultimately kill the replayability of this game. The 'runs' take long enough you get invested, this isn't really a roguelike as much as you may view it as one. The runs are too long and the game is too punishing if you don't load.
Gearing the game towards this idea of restarting just suggests there won't be enough content/story in the game to make a good sandbox and that's what you really need. I really hope you reconsider the direction of the endgame.
Suggestions
-dynamic "boss" ships that are up armed, high level captains and have unique skins
-dynamic "special" weapon generation, use a number generator and base it off player level
-dynamic "encounter" generation, more reasons, people, fleet types, places for stuff to happen, give to universe more life
-stretch your story legs with directed chaos, make the story fun in a more dynamic way. Instead of go there do this yay win, how about go here try to do something and depending on what happens the story goes in that direction. Have that direction affect things
-unlimited level cap with late game options opening up increased fleet and engagement sizes as well as simple things that let you specialize more. +speed +colony tax +signal damping +smuggle chance +manouv +vent speed and so on. Can also make enemy engagements much more unique. Opens up surprisng battles that need to be repeated. Means people can't just play super safe by avoiding dangerous ship designs.
Honestly the list goes on and on and your better off just adding *** loads of fun stuff and then balancing it based on feedback. People will have so much fun and can get really invested in their mad setups and long sector conquerin campaigns.