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You could get invaded by pirates or the crew could hate and kill each other.
Artstyle was pixelated and it had an isometric view.
Sadly searches for "spaceship" , "ai" and "crew" have not been fruitful
The Away Team fits some of your criteria:
https://www.gamingonlinux.com/articles/exploring-space-and-avoiding-hazards-my-thoughts-on-the-away-team.10606
Destination Ares is out for Windows only:
https://www.gamingonlinux.com/articles/destination-ares-control-an-ai-aboard-a-rusty-old-colony-ship-and-keep-the-crew-alive-linux-support-is-planned.8534
AFAICT, Universe Edge never actually released at all:
https://www.gamingonlinux.com/articles/universe-edge-a-spaceship-building-crew-management-space-exploration-game.3395
Any of those ring a bell?
Graphics were a BIT better
THAT IS THE ONE :)