I've a pretty simple idea which could make the game a whole lot more immersive and scary. (This is a suggestion for the steam release)

Ship tilting/pitching. Being able to actually adjust the pitch of the ship would be a very cool feature. Especially for hitting rocks or being attacked by large creatures. Simply being smacked while locked in the X-axis is a little bit boring, don't you say? I think it would be cool if the ship actually was rocked up or down when it was hit and made to tilt. It could even get to the point where the ship could flip entirely upside down perhaps. I think this would make the game a good deal more intense when things strike the ship, having the difficulty of moving around while the ship is shifting and or at odd angles.
The diveplanes could be controlled from the control panel, perhaps with the movement control keys, or even a slider to fit with the mouse-only nav panel interaction.

Another thing to add to this would be improved water physics. Having more water in the front or back of the ship could weigh the ship down, and having a hole somewhere in the ship would let air out and have water replacing it, tilting the ship from the force. Things like explosions, etc. It could also be cool if when struck, or there's an explosion, etc, that the lights may flicker and electronics may be interrupted for a second.