Hi, I am a newone in this as well, and also have a dream... but I am with the fellows, for the first time, keep it simple .
What I am doing for my first sub (scratch Akula 1/96th) is using a microcontroller (87C51 FA) to act on diving and surface operations, including helms-man functions (acting on the planes) and controlling the inclination of the whole sub. Also the micro will control the motor speed (via Pulse Width Modulation). Other functions will include up to 16 on/off switches, water alarm, lost of signal alarm, emergency buoy release. But when trying to put a camera, sonar, etc, in a sub... I think the matter can get too complicated very rapidly for a standard RC sub. I have been researching a bit and I am thinking that perhaps using a computer to control the whole stuff may work (for me will be certainly a (long) future proyect). A powerful wireless modem may well be the way to link the computer with the sub (I have no idea of frecuencies availables and legal stuffs), and the link could transmit the camera images, the sonar digitalised info (allowing post processing in the computer using matlab or something of the kind, beamforming, etc) and obviously many data about the sub status (RPMs, water temp, motor temp, battery charge, depth, bearing, etc)... But better start with a simple RC sub, using an stardard RC Transmitter... even if you put a camera in it, there is plenty space for upgrades (directional antenas, transmiter booster, etc).
By the way, welcome!