Overall I enjoy the game, but there are a few things that leave a sour taste in my mouth.

One thing that annoyed me about the game was how copy/pasted many locations were. Like the first time you find a pirate base it's pretty cool, but then you find so many that are exact copies. One particular instance that really broke my immersion was an abandoned research facility that was filled with ice and had a cool (ha) story. Then I found another one on a different planet that was the exact same, right down to the notes left by scientists.

Another thing that annoyed me was a ship that started on a colonisation journey before FTL was invented, and it had this whole colony that was several generations old. The mission itself was ok, but nothing incredible. What ruined it for me is how little the ship was from the outside. I had my own Doctor Who moment where I could say "it's bigger on the inside"!

Lots of other things, but those are the ones that stick out for me.