I'd like to see all of the controls that normally use the numberpad be bindable to something else.
The reason being that I intend to build myself a nice little controller for Naval action (with some three way spring-loaded switches for the yards, a pot for the wheel, and a number of buttons for things like deck locking/ammo type/repairs/crew mode), the ability to simply have joystick buttons for those number pad functions would greatly simply things for me. Selfish, but I can't be the ONLY ONE-well, maybe I am.
Some more minor things.
An option to flip the windpath arrow around 180, most weather-vanes in the US point into the wind, not with it, I STILL get myself flipped around now and again. Bearing numbers might be nice.
A little Tilt indicator might be nice, but is not nearly necessary.
The ability to name ships is probably impractical, but would have it's uses. Also, I'd note that I'd be tempted if alternate skins where sold for the game.....
These are just a few things that I've been considering.