I too would like more "depth" to the ship damage model. I would implement the following changes. First, add a tanker to emulate fuel bunker at land bases; add an ammo ship to emulate ammo bunker (these two ships could use the same ship model, i.e. a Liberty ship, as there were tanker and cargo versions of the LS); a troop transport (could also use the LS model); an LST to take place of vehicle hanger. The following damage effects would then be in affect:
Damage Affect
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CV deck = No planes launch
Tanker damaged/sunk = A/C and vehicle fuel limited
Ammo Ship sunk = Ordnance unavailable
Troop sunk = No troops
LST sunk = No GV/PT
If this is too many ships to add, you could combine the fuel/ammo/troops into a single Liberty ship, with each one independantly target-able/destroy-able (the cargo hatch covers would be your aim points).
Finally, the fleet commander should be given the option for direct helm control and the ability to set fleet speed to slow, half, full, and flank settings. The fleet speed would of course affect how heavy and aircraft you could get off the deck. Make it so the fleet would go automatically back to following waypoints after a set length of time with no direct helm inputs.