Small bump. Been doing some idle thinking over the days, and think I'm going for a room-based setup. The ships are split into different rooms, which are literal divisions between floor spaces. Each room tracks its temperature and air pressure, and if the player desires can track its own crew separate from the global crew. This way you could have specialized engineers but your 20 gun ports are manned by below-average mooks. Heat would transfer from one room to another, based on how many walls they share and what the walls are made of. Radiation would mostly spread globally from its source, unless a specific room or direction was shielded, so it wouldn't follow room designations.
Crew is the next issue to me. 'Normal' crew would be generic labor from the docks or barracks. They must be fed and payed, from the ship's inventory and from your credit stack. 'Conscripts' might come from an area with required military service, where you must feed them but not pay them as much, and would be poor, with -1 to dice rolls, for instance. 'Slaves' could be acquired, needing only food, but have obvious problems, like chances of rebellion/subterfuge, and other people disliking you. Certain plant-like crew might be gained, not needing traditional food but they still want money. Or perhaps robotic androids, or just no crew and run it all on automated systems, which would be cheaper, but require higher maintenance and not be as flexible.
To keep things simple, one room could have one grade of crew performing a job, grouped as one cluster. For instance you could have a gunnery crew of 4. One is a spotter, one is the shooter, and two handle loading and maintenance. But they aren't handled as individuals, they're treated as one cluster of +2 spotting, +3 shooting, +1 reloading speed, +1 repair rate. If you decide you need to add someone new, because you need a new spotter working, then you'd average their skills out. So that 4 becomes 5, and your new grade on spotting is 4/5 of what it was, so it's only 1.6, and your shooting is now 2.4, and load and repair are .8. But if you brought in a new spotter who was already grade 2, then the spotting would remain at 3, because it averages the same. If a crew grouping has dropped in value, but is still relatively close, it'll regain at a higher rate back to what it used to be - retraining is faster than new training. But if too much of the crew is lost and replaced, or if you add too many at once to a group, then it takes a while to train everyone up. Additionally, moving crew from one area of the ship to another existing area puts a morale penalty - if you think you can meta-game by moving crew around and playing with averages, you just get dice roll penalties for a while anyways.
Because crew is separated by rooms, you can have a group of crystalline entities working one of the weapon rooms, and if there's a hull breach they won't die from loss of atmosphere, while further in the ship you have a group of humans working engineering because they're great engineers, and have a group of aliens working on piloting because this particular ship isn't maneuverable and you can get cheap alien crew who's not very good.
TL;DR - You can have a 'global' crew that works across the ship, or have 'room' crew in specific systems. Crew ability, feed rate, and pay rate change by race and by skill level. Crews are averaged, without individual units.