I always thought it would be cool if once you sunk a task group, it would need to rebuild at the docks, and you could attack the ships at anchor to keep the Task Groups out of action longer.
I know alot of people will poopse this though 
Ever commanded a task force and while setting the course got the message "Way Point Touches Land?" and the way point line was out to sea?
Because of the way the tiles are drawn, the shore area is actually a blue land tile, which precludes the ability to put ships in that close.
But it would be cool.
I also like the idea of mannable Ack on the ships, but I think the ships are actually ammo bunkers with the ship shape assigned to it.
No reason why there could not be more mannable guns around the port area, though.