I think the problem with water levels in most games is threefold.
1. Control. In a water level you are usually out of your depth, and the control you have over your character will often feel clunky and misguided. Nobody likes the game to suddenly remove the ability to move quickly or evasively, unless it replaces it with something to make up for the loss of control... like a harpoon minigun, or something.
2. Enemies. I hesitate to use the word 'learning curve' because the game isn't getting more difficult, per se - it's just rapidly changing its playing style, and, if you'll forgive the metaphor, we don't like to be thrown into the deep end without some instruction. Fishy and amphibious foes usually take different approaches, and we feel somewhat cheated that we weren't given more warning when a lamprey jumps out of the slime and latches onto our fleshy unmentionables.
3. The environment. Level designers seem to run out of ideas when it comes to water levels - even Half-Life 2, a triumph of design, would occasionally shove you into a tiny grimy drainpipe with no distinguishing features whatsoever. Segments are usually confusing to navigate and, of course, the 'shortage of air' mechanic ensures you have to pause every few seconds to refill your lungs. Nice way to break up the flow of the entire level.
So, tl;dr: you're swimming around a dark tunnel, you can't see for shit, you're moving achingly slowly and then you get killed by some fish thing you never saw. Sounds like Serious Sam to me.
