tough question to be honest.
Not a lot of the smaller cameras come with full manual control over things like shutter, noise, and iris. Instead they have "exposure compensation" which isn't really the same thing.
So, to learn things in the full manual mode your options are limited. ALthough, it is not necessary to shoot in manual to get quality results, you will have more say over things like depth of field and gain (noise) etc
There are a lot of good cameras giving good results at the moment.
What sort of price range are you looking into?
Some suggestions for cameras to do some research on are:
Sony HC5 and HC7 (brand new, not tested under water)
Sony FX7 (again, not tested underwater)
Canon and Panasonic also have cameras in this area but i am not so familiar with the models, i am sure Drew can chime in on that.
Also, for any UW setup i would really suggest a housing/camera combo that gives you access to manual white balance. This is a huge thing if you ask me, especially if you don't want to spend hours on post processing trying to extract the colours in editing. Also, you want a housing and camera that can give you manual focus.