It may be too far along in development, but here's my idea anyway. In real life the captain would not micromanage the crew. He has officers for that. The second in command typically deals with crew issues.
I suggest that, like SH series, there are officers that the player can assume control of. He controls one of say, four men aboard, with an AI to handle the other three until he switches.
These could be the exec, engineer, captain, and the German equivalent of chief of the boat. The captain can influence things with orders and queries to the other three, or he can switch to one of them to more directly control an issue.
Just thoughts that
could eventually lead to a multi-player coop version with four players per boat.