Wow, I have been planning to make this exact thread for a couple days now.

I believe that one reason can actually be something as simple as the fact that water is an unnatural habitat for us.
When we navigate water stages we have to control the characters in a way that feels less intuitive, because we haven't evolved for living underwater, which can make it hard to control the characters properly.
This could also be the reason why a lot of us tend to prefer plain/grassland stages - they feel more familiar to our land-living brains, and we feel more "at home" on those kinds of stages.

However, I do actually tend to enjoy the atmosphere on water stages.
I don't think anybody can deny that the underwater stages in Donkey Kong Country are incredibly beautiful and soothing, and the music on those stages adds a lot to that atmosphere as well.