What's particularly important to me is that crew should be able to be injured and killed in action. A complex, in-depth crew system will feel incredibly game-y if the crew can't die as a result of battle. This could be used to incentivise surrender and escape from battles - if you escape, you save your crew. If you surrender, your crew can be paroled so you can take them on your next ship. You sink? Goodbye to all your well-trained officers! I think it'd do an awful lot to reduce the suicidal nature of combat as it stands currently.
I like the crew system from Silent Hunter 3, where crew have randomised names, and the player is able to purchase passive skills (Navigation, gunnery, repair) which add efficiency to the applicable action) with the universal "renown" currency. This currency is earned by sinking enemy ships, reaching assigned patrol areas, etc. Crew are assigned to compartments, and damage to those compartments has a chance of injuring or killing crew outright.
A neat management system could also be implemented - you have x number of men and officers, and maybe could drag their icons around to fill out a watch rota to maximise efficiency in areas which are most important to each player.
The SH3 crew management screen: