Personally I would like to see a game played mostly from first/directly over the shoulder third person, centered on the player's character, and then directing your crew through a command interface. Much of the actual details would then be handled by predictable AI manning the key positions.
Set your heading, and the helmsmen makes the most logical turn, and your officers order a suitable setting of the sails during the change.
Captain wouldn't normally be the one aiming or giving orders to fire, but rather stepping back with higher level orders: What type shot, give the gunners goals, and the gun crews do their job. Captains job is to manage the ship as a whole, not to be bothered with trivial tasks. Order the guns readied with solid shot for a long range broadside targeting a given ship, give your helmsmen a heading that brings your guns to bear on the enemy target, and when everything is suitable aligned the gunners fire.
Order a boarding party ready, and the men line the decks. (If things are obvious, ie, only one ship reasonably close/only the one ship selected as a target, then user shouldn't even have to state boarding from port or starboard) Ideally I would like to see a pirate game simulating realistic boardings, but that would be a tough AI and physics job to pull off reasonable well.
Personally I would want to play a game that lets me see and hear only what a real captain would.