to support an open world, you will have to consider timing issues, short cutting travel, etc... I.e. once you commission a new ship, it could take months before it shows up.

In WWII, one consideration might be paving an airport on a tiny island. In WW2, these pacific island airstrips were vital for shortening the distance for aerial attacks. But it meant intense battling to gain and control airstrip worthy land. But once that is done, it makes sense that you would be "granted" control of a carrier at that time.

Additionally, you could start lower in command, controlling a destroyer in a group of ships. I.e. have plenty of battle going on, but you get isolated objectives in battle, and can witness larger ships and strategies. Then as you do well, you rank up, and control more ships, and get sent on missions where you are given more control.

Additional objectives, taking over an island airfield with as little damage as possible. (make it useful sooner) aside from repair time, you have the expense of fixing it. money that could be spent on more weapons/troops/vehicles.

Also, Moral could play a major part of it. after a good victory, (or island party to unwind) your sailors are refreshed and feeling more confident and capable, will handle better, aim better, react faster.

It could also be that if you are commanding a large force (many ships) your strategy plays a major role, but the ships still have their own decisions internally. They will try to follow orders, but sometimes its just not reasonable. And that point where they decide to do their own thing could happen sooner if your strategy sucks.

Maybe you could also "claim" ships. I.e. take them over with out sinking them. By focusing on weapons, then boarding. You could use these pirated ships to launch sneak attacks, gain intel and more. For instance the longer your pirate ship goes undetected, the longer you get advanced messages about the fleet. I.e. they still trust their decoding devices.

perhaps you could also have time commanding a variety of lower level ships. After piloting all of them for atleast X time or missions, it opens new missions for you, I.e. This mission requires 2 destroyers, a battle ship, and 20 transport barges. You need time commanding all of them, before you get to control them all at the same time. (maybe not the barges though, or the missions with them would be smaller, like loading/unloading, docking, etc... Particularly navigating an island shore to get vehicles unloaded.)

I also like the idea that at any point in the game, you can focus on a particular craft. (boat, plane, sub, tank) and take control, at least in some part.

Another goal could be Reward for confirmed kill. I.e. you've become well enough known that your enemy's are targeting you. Additionally Reward for confirmed kill could be reversed. I.e. Bounty for enemy npc's.