vopap,
Ypu sure have your work cut out for you, but it is possible to get this done. It is ultimately the best to use USB since it requires only 4 wires and can transmit data many hundreds times faster then the serial or parallel port. The protocol is actually quite complex, but it would be useful in the end for a nice flexible interface.
You need to use a microcontroller for the data packet handling and etc., it would be the best choice. It is best to make this sort of thing easily expandable so you can get fancy in the future with it. This could include more processing power, power supply capable of supplying more current with extra connectors, high bitrate capability, space, etc.
The design is actually very simple. The great thing about working with subs is that you can add all the weight you want at virtually no expense. I would use lead acid batteries, which offers a cheap reliable source of power. You need to get a water pump that can generate a fairly high static pressure which the limit is determined by the maximum depth you wish to take it. The simplest design would be to use a rubber blatter and fill it initially with a fixed amount of air. Then you would pump in water to cause the sub to weigh more. If the balance is good, you should need to pump very little in for it to descend.
A depth sensor is easily made with some mineral oil in a flexible tube with a pressure sensor. This will give you a linear voltage to depth ratio which you will have to interpret to real units by means of a microcontroller.
If you were ever thinking of radio to control this, you will need to remember the rules of radio and how it works. In any medium, the higher the frequency the more the attentuation. In water, the attentuation per metre is extremely high. The lower the better, but this limits your bitrate severely though.
I have been babbling on for a while,.. if you have any questions, I will be glad to help!
Steve