Water allows for a bunch of irritating mechanics that people hate:
- Raising and lowering water levels, which often takes lots of long schlepping around routes you've seen before.
- If it's a game where you die if you land in water, it'll be a high-death, hard-to-platform area.
- If you have an "air meter," you'll probably drown a lot because the area includes at least one "barely make it" tunnel that most people won't make.
- As in real life, moving in water is clumsy and slow, and you'll blunder into enemies a lot, or down the wrong path, and swimming controls have never been particularly amazing.
- You usually can't fight well underwater, meaning you're at the mercy of said enemies.
- My personal pet peeve about water is that most of the time, characters can't leave the water unless there's a platform at water level to climb on. Why the hell can't you go underwater, kick really hard, and "jump" out of the water, then grab a ledge by your hands, hang, and pull yourself up? It's like the chest high walls in Metal Gear that Snake couldn't pull up onto. Why the hell can't a super-soldier get out of the water so long as he can manage to reach an edge with his fingers? This problem leads to a lot of slow, clumsy meandering through water until you find the two feet of space where you can actually get onto land, then try your puzzle again.
Also, people hate water because of the Water Temple. That's probably half the reason.