...but water levels are my favorite ones... maybe I'm just playing the wrong games. Or actually, the right ones.
There is a lot that water can do. And the ability to change a set of gameplay mechanics while keeping them in context is (if done correctly) a neat way to make a game varied.
To use oxygen meters can successfully give a time limit.
To impact speed can give the requirement to foresight in attack evasiveness (rather than reflexes).
Water puzzles are plentiful and can allow for lots of stuff (depending on the developers' creativity).
Impacting visuals can add the requirement for the player to give extra room, or know movement patterns of objects better.
Swimming can enable a character that would otherwise move predominantly on a flat plane to move in all directions.
It can provide differentiation in mechanics between the ability to float and sink.
Varying levels of reflection can add to an area's sense of depth or environmental illusions.
Varying levels of turbulence can indicate weather changes, and give dramatic changes in feel to a place.
It can require more perception, should one have to retrieve something from water when outside.
It can provide a new range of baddies (or goodies).
And so on.
And because of all this, I imagine that developers get very excited by the production of a water zone, at the expense of the player if not properly examined. Kind of like when an indie movie sucks, but the maker says that you, as the viewer, just don't get the message.
Although, in terms of complexity/puzzles, I think the Ice Ruins in the new Zelda:aLBW could give OoT's Water Temple a run for its money.