I might suggest that players be able to hire A.I. Captains of varying skill and expense to command ships in a fleet rather then having to move them around personally. When combat engages, the player as the Admiral of the fleet, directs the action and can issue orders as normal but also set broad priorities like "aggressive" to make Captains engage all nearby enemies, "defensive" to cause the ai Captains to hang back out of the action and engage only when being attacked, and so on and so forth. Under normal circumstances, Captained ships won't just sit there but move around and engage as their priorities allow.
These order would be carried out with a competence that is commensurate with the Captains skill levels. These skill might include "command" a Captain's overall leadership of his crew. A Captain with a bad command score could receive negative crew effects such as slow command cooldown, slow crew actions/reactions, and/or a chance for mutiny which turns command of the ship over to the enemy. Another skill might be "navigation" or how well a Captain can navigate his ship and avoid slamming into friendly ships, rocks, he ground, etc... A good navigation score could mean a positive bonus to speed and a bad score a negative. Yet another skill could be "gunnery" with the obvious bonuses to gun speed and accuracy and a bad score could negatively affect speed and accuracy and allow for a percentage chance of a gun crew blowing themselves and part of the ship up. Other skills might come to mind but thats a start.
Captains may also bring with them very unique items that bestow bonuses(these can vary from just the captain's ship to effecting the whole fleet) such as "Blackbeard's Spyglass" that increases his ship's or the whole fleet's gunnery accuracy or perhaps a "Suspendium Purifier" that increases his ship's lift. Etc, etc, etc... All these variables - skills, unique items, etc... will affect the Captain's salary. Availability of Captains could vary from time to time and city to city. Finding a rare Captain could also result from a random event as perhaps a percentage chance when conquering an enemy city or whatever.
Just some thoughts.
That's a good idea, even if I think that, just like in "design and combat", you should be able to turn A.I. on, it's too hard to control 10+ small ships in a large scale battle, maybe just for the ships you selected, don't want my 3k ship going back and forth trying to attack a 300 one.
I think it works in every combat situation, even in the strategic mode if you can toggle AI off and on for each ship as needed both in the fleet management screen and when you click on a ship during combat. Any ship without a Captain is forced into manual mode until one is hired. Then if you decide later that you need manual control over a specific ship or all ships, you can toggle them off as needed.