It seems underwater in AC4 will be what naval battles was to AC3
"Jean: We will have some areas, yes, where you will be able to go down underwater, using the diving bell that we saw in that trailer. So it will be really focused on limited areas. I would say it’s almost the same strategy we had with the naval experience on AC3. When we want to try something new like that --to bring something to the franchise-- let’s first make it good, focus on it, deliver it properly, and see what we can do, and then “why not... who knows what after?”, but in our game, we will have dedicated places for that."
Check this out near the end of the interview http://www.ausgamers.com/videos/view.php/71694
Edit:You also have to buy the diving bell to go underwater