This has probably been suggested a million times, but...
I've been thinking I'd love some kind of morale mechanic for my crew. If I lose a fight and run, or prey on weaker fleets, I don't think my men would respect me as much as if I won against larger fleets and fought defensively. Also, I think they might get *** if I eject half of them in the middle of a neutron star system because I picked up extra crew from a derelict but didn't feel like paying their salaries for the rest of my exploration circuit. Or if I hire a bunch of crew and then turn around and blow up the station I hired them from. Or if I keep them right around a skeleton crew level because I'm a cheap bastard, so they never get to take any R&R because they have to work 12 hour shifts to keep their ship combat ready. Obviously they already leave if I don't pay them, but I'd like the ability to pay them more and increase their loyalty, so they'd stick with me through the hard times. Seems like morale could get involved in all these places.
Of course, if I embarrassed myself as a fleet commander and my crew no longer respected me, I could fix it by firing them all and rehiring a new crew, but that's already expensive due to existing systems in the game. I know Starsector used to have more detailed crew mechanics and simplified them (crew experience) but they feel oversimplified and commoditized. But I feel like morale could be abstracted and be a good way to provide feedback to the player choices above.
Secondarily, some more distinctions between crew types would go a long way -- for a game where the item types are divided between supplies and food, ore and transplutonic ore and metal and transplutonic metal, luxury and domestic goods, etc. for all space crew to be a single undifferentiated item seems a little weird. Why not fighter pilots, mechanics, and bridge crew? Pilots might cost a lot more salary and be rare because they have an incredibly crappy job. But maybe I just want some kind of impossible HR management sim in my space WWII gunboat game and I'm weird...