This is not my field, but il throw out some thoughts anyways.
The SBC got the 8/8/8 , ethernet controller and a usb hub on board.
This ables you to hook up a web camera, 8 different sensors, 8 switches a controller for the motors etc.
The ethernet controller can be used to switch the unit into a ROV when needed. (In addition to data transfers when docked of course)
The 1056 could be helpful in navigation with its compass and accelerometer.
Add a usb gps and you are ready to go