A few more (not well thought out) ideas
There could a be a non-permanent degradation that occurs to ships if they are not repaired in docking facilities. So, if you fight battle after battle your ships slowly accrue non-permanent' degradation until you dry-dock them in repairing facilities. This could just be a lowering of max recoverable CR until you dry-dock.
I really like Cyc's suggestion. Permanent degradation would occur on salvaged ships. After battle, you can stick around and attempt to salvage ships that were disabled during the fight (each salvage attempt using in-game days). Any ship successfully salvaged gets a number of negative hull mods, disabled weapons mounts and/or severely lowered stats. Permanent degradation can be removed in dry-dock for a large fee. It's up to the player to decide whether they want to salvage that ship (and risk sticking around), whether they can then just use the ship as-is or whether they want to pay the fee to restore the ship to original stats.
As for crew, at the moment I don't really feel like my stack of crew in the cargo screen really represents the crew for the entire fleet. They seem more like a cargo of which I have to have a specific minimum of all the time. Some ideas:
- Crew minimum could just become Crew
- Crew maximum could become passenger space
- Crew just becomes another stat on the hull rather than a cargo item
- Buying new ships comes with a full Crew stat
- The Crew stat is lowered in the same way that crew are currently killed in combat
- If the Crew stat becomes low the ship gets a reduction to stats and/or max CR
- If the Crew stat becomes too low it gets mothballed
- The Crew stat can be replenished when docking at a market
- Add a Crew Experience stat to ships (represents the level/efficiency/knowledge of an entire ships crew)
- A higher Crew Experience level raises the max CR for a ship
- Crew Experience is increased for various actions (combat, flying, salvaging etc.)
- Crew Experience is decreased when signing on new crew (but perhaps you can pay more to recruit a more experienced crew member to keep the average higher?)
- Crew can be transferred from ships in fleet but lower the Crew Experience stat
EDIT: Forgot to actually say what Crew Experience stat does... zzz...