Sorry if this has been suggested before (it probably has), and apologies for the poor formatting/lack of coherence for what you are about to read.
What if you could hire randomly generated crew members from ports. These crew members could come in the form of Surgeons, Quarter Masters etc.
Similar to World of Warships where you get a Captain and then you can tailor his 'Skill tree' to match your game play style, you could level these crew members up to match yours or the ship your are playings style, the crew members could level up with you and could be transferable from ship to ship.
I also recall a similar thing in Expendition Conquistadores where you can find/hire people to join your expedition.
Or perhaps forget the skill tree and just have them give static bonuses, I feel it could still give the player more of a 'My crew is my crew' feel. At the moment my crew are just numbers on the screen.