I think the only problem with the DKC water levels was that the fancy graphics made it hard to tell where the platform edges were. That was a problem on land, too, but the roll-jump mechanic made it easy to deal with. Underwater, however, Rare required extra precision from the player without returning the favor. When trying to figure out whether or not you could squeeze between the wall and a shark, that could be frustrating. However, I think it's the phobias underwater levels trigger that make some people hate them. I don't think the DKC ones had that effect on me, but I understand the sentiment.
I liked the DKC underwater levels, but I won't mind if this game lacks them.