As someone who likes to compartmentalise his ships I find it very frustrating that after any sort of fight, that does moderate to a lot of damage to my ship, that after I repair I have to sell all of my crew and then rebuy them (costing a good chunk of resources) to return them to their bunks in the correct amounts because people have navigated across the ship when it was damaged into parts they couldn't normally reach. It means I have weapons not firing and far too many on engines for example.
The easy way to fix this would be to have a button that returns crew to their bunks. This might just be a feature or you could have a 2*2 room teleporter that returns people to their bunks. This could also be the start of boarding combat but I think that would be very difficult to code.