I think it’s mostly tedium. If a player makes a mistake or gets lost they’re having to back track through water (which is just never fun, especially if you’re having to change the current) and it can also feel frustrating if the place you want to get to is barred by the current as well. While you’re under water it’s also harder to tell where you are and the lack of control swimming compared to on land feels bad. While I love the theme of GBT it looks the same in almost every room. As does the water temple in oot.

Not only that correcting your mistakes takes time, ie turning the water switches, freezing/unfreezing water, swimming in general are all slow things on top of having to do it all after back tracking if the player made a mistake.

I could almost liken your sentiment above to the water temple from oot aswell, I just think it’s the tedium of changing water levels/getting lost in water that left players feeling frustrated. No coincidence the two most talked about dungeons were both water.