Well, just for whenever we DO cross that bridge, the main ship idea worked around the type of map and hence the tactical role of the ship for that map.
Apart from miniturisation which is a stretch, I know, although theoretically possible.. very theoretically so, for general maps, the aircraft carriers would be created like the bridge in Vanilla.
The main body would be like aircraft carriers in Vanilla, with the actual flight deck being destructible so that defending the carrier would not be about preventing it from getting sunk, but getting rendered useless for aircrafts to take off from. Be it steel lie the Japanese carriers, or wood, like that of the Americans, bombing it continually would sooner reduce it to ribbons, taking out one stretch for aircrafts taking off, and further on until no aircraft can take off past the gaping holes.
With a static main body, you would be able to see right into the cabins below. A similar design could be used for the Battleship such that scout planes can still take of from it. The differenct is, with this ship, it would have useable gun positions which can individually be disabled. Hell, we could even blow a hole in it which could set shells, using the same code as explosive barrels, and which could start a fire like that from the flamethrower that leaves high plumes of smoke and kills personelle on the ship by sheer proximity.
Smaller ships could be done like in Red dawn, drivable, with no vehicles on it, and only spawn points for gun positions, with exiting putting you right in the ocean, or prohibited completely
Amphibians for transporting tanks etc, could work using Red Dawn's tactic of 'towing' the vehicle, that would then eject itself once it starts moving, hopefully when the ship has come to a complete halt at the beach.