This would pose several issues.
1. Distinction would need to be given to specific crew members.
2. What happens when a flagships is captured? Right now the game mechanics reduce crew size to minimum required to sail k believe.
3. If flagship is captured is the crew with abilities captured as well?
Right now a crew is tied to a ship. If you sell the ship you lose that crew. They are not available in some staging area. You must hire an entirely new crew to sail new ship. This would require some sort of crew transfer system.
Honestly I think this makes things much more complicated than it needs to be.