Recently, a lot of players (myself included) have been using ships with detachable crew quarters to save weight/space. I think this is a really cool strategy, but I don't think it's something that really makes sense for the game as a whole.
I think there are 3 general ways to change this:
1) make it physicaly impossible to detach crew quarters
2) remove crew quarters altogether (perhaps to return in a future morale update)
3) make crew quarters necessary for crew
I'm in favor of #3, making crew quarters necessary for crew, and I think a possible way to achieve this is by adding crew fatigue. Here's how it could work.
As crew carry around batteries/ammo, they accumulate "fatigue." Picking up and setting down batteries/ammo creates extra fatigue. Periodically, crewmen have a chance to become "exhausted". The more fatigue the crewman has, the more likely they are to become exhausted. When a crewman is exhausted, they cannot take new jobs (they'll finish their current one) and must rest at a bed in a quarters/bunk, rapidly reducing their fatigue. When fatigue reaches 0 they are no longer exhausted and can start working again.
If a crewman becomes exhausted and there are no available beds, they rest where they are until a bed becomes available. In addition to congesting other crew, crew resting without a bed reduce their fatigue much, much slower.
Idle crew no longer go back to crew quarters. Instead, they go near a reactor/factory/storage and rest until their next job (and reduce their fatigue at the normal resting-without-a-bed rate).
Crew do not gain fatigue while walking around or manning a room, only when carrying something heavy.
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I think that the exhaustion-rest cycle should be very long - crew should (on average) be able to work for several minutes at 1/2 speed and then spend 30-60 seconds resting. Of course because of the randomness some crew would get tired very rapidly and some crew might last 5+ minutes without exhaustion, but that's a good thing because it prevents all your crew from getting exhausted at once.
The number of beds per bunk/quarters would probably need to be reduced, so that each crew room barely provides enough fatigue recovery for it's amount of crew. So maybe bunks could have 1 bed (still provides 2 crew) and quarters could have 3 beds (still provides 6 crew). On real-life warships it's fairly common to assign 2+ crew to the same bed (maybe the beds now come with fancy medical equipment which takes up the extra space).
Visually, fatigue could be indicated by a red face, and exhaustion could be indicated by a blue face.
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Hopefully, this would achieve a number of good things.
1) detaching crew quarters would be very situational
2) crew quarters would have a purpose instead of being dead weight
3) parts would no longer suffer alpha strike delays (where crew has to walk from quarters to a reactor/factory/storage)
4) carrying batteries/ammo short distances becomes slightly weaker in comparison to long distances, which makes it easier to centralize things (e.g. big reactors)
5) fast ships that run their engines 24/7 will need to spend more on crew to make up for exhaustion
6) it makes sense - wouldn't you get tired carrying around massive cannon shells all day?
This would also have a LOT of unintentional side effects, since literally everything runs on crew. It also adds complexity, though hopefully it's not too hard for new players to get the hang of ("Crew get tired from carrying stuff around. Tired crew need to go rest").
There's probably a lot of problems with this idea, so I'd love to get some feedback.
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Some alternative ideas to make crew quarters necessary for crew:
1) crew carry around oxygen masks, and need to refill them at quarters every now and then.
2) quarters provide ship-wide life support, and if there aren't enough quarters the whole ship/compartment slowly suffocates.
3) crew are androids/cybernetic - and their "quarters" contain their control unit so if the quarters die the crew die.