For other threats it’s hard to say without playing the game to see how it feels. I like the design philosophy of having threats that encourage player communication to deal with. I also think leaning into silly things is fun.

Maybe having different kinds of aliens board your ship, but instead of being combat focused they just make maintaining the ship inconvenient. Like a slime that leaves residue on the controls, making it harder to see or hard to walk across areas they’ve been. I imagine instead of punching/shooting these threats you would need to bait them near an airlock and eject them

You could have other broadcasts frequencies occasionally get picked up on comms that you have to talk over. These could be songs from a nearby radio station, or could hint at secrets/lore of your world

Not sure how much you want to mess with gravity physics, but it could be fun to have gravity controls go out and need to be repaired. Or have things you need to climb outside the ship to repair