I dislike the insta-repairs, the 'holomes' and the lack of real death.
If a ship gets damaged, I'll either keep it damaged, or put it in for repairs & leave it for a day, & take a different ship out.
Instead of a magically reincarnating commander, I have a 'gang' of 9 characters, with a ship each, and if a ship gets blown up, the commander will be dead, and I'll generate a new holome commander, complete with mini back story.
I also like to imagine that 30km/s is the max speed things travel in systems, and the supercruise (above 30km/s) is actually a sort of cryogenic susspension, where you effectively 'sleep' until you get there.
I do need to ditch that theory occasionally though, when a destination is 100kls away.
I also like to fly FA off, even if you have to land really slowly. Slightly awkward on a game-pad, but I'm getting better. Still can't land high G planet bases with FA off though.