The graphics of landing, being rotated (though I don't know why a spaceship needs to be rotated), dropped into the hold for outfitting are all nice, but then you click "repair all" and bang, all done. If this is a hyper-realistic game, then make it take time to load (show a cutscene of cans being loaded), refuel (graphic of that), and repair (something like how Mechwarrior 3 did it with sparks flying but some kind of metal cover or robot over the damage so you don't have to show a graphic of every detail). Not a lot of time, just a handful of seconds, but repairs can stack so that 90% repairs made to every system take a lot longer (say, a minute) than just a 20% hull repair.
Honestly, I'd like it to be more like Frontier where you get out, meet a port agent quickly, and then go around the base to places. Just cutscenes like embarking, walking to elevators, walking into a bar (for smuggling) would all be good.
But, for sanity's sake, there should be a "skip" button too.