I love the command arrows idea.
Those arrows could be enhanced with the dropdown order attached to the arrow idea by NorthernWolves.
The commander could choose to not use arrows and just go with some generic orders for ship clases or specific ships and leave the rest to the captains of those ships or to just give a basic order to the fleet (flee, line, melee...).
The incentive to following orders should be an increase in your "loyalty" skill independent of the fact if following the order makes sense or not.
The "reputation" skill would be some calculated number that puts in all other information (loyalty, rank in navy, win/loss, prize money, sailing, navigation, gunnery....).
This reputation skill could allow you to lessen the cost of ignoring orders (the hit to loyalty would be less for renowned captains when they are successfull).
Reputation might have a lasting effect on your crew morale.
Crew morale might affect several stats that are "crew operated" as already pointed out by Horatio Hornblower
-reload rate
-execution of sailing commands
-fighting power in boarding/defending boarders
-waterpump speed