I generally like non-mmo games like the Starsector that have the possibility to be (or make yourself through leveling) The Badass Main Character, not some other non-AI controlled but otherways absolutely miscellaneous entity that thrives to survive and reach some goal. I like that AI captains being inferior to the allmighty insert_your_nickname_here, I like the idea of being about 50 levels above AI level cap, like some damn demigod, the ship that is piloted by the Mighty Leader is faster, stronger, gets more ordnance, guns/range/damage/fire rate, get yourself a Hyperion or Paragon, guns blazing, go slaughter the entire enemy convoy, ending unscratched, say "I'm not impressed Hegemony/Tri-tachyon/whatever"
Hope you can see what i mean.
And now I see: here you go, have this level cap, oh, AND it is dangerous to go alone, take this (gives me the damaged Lasher), also your skills will be less OP, go get some more Lashers if you want to fight someone besides pirate faction. Also your solo Paragon will have n% less speed and range.
But seriously, i believe that those overhaul will make game better, or at least more of what Dev see it to be, the problem is I think there should be a chance to have something for those who like the game as it is now.
TL;DR
Could you just add a little option to have not mod but just ingame option
-set level cap (default(40) - custom - infinite)
-set the impact of electronic warfare and maneuvers (n% weaker - default)