Because now that we have great graphics, desolate/muddy areas that evoke emptiness can't exist. All games must have detailed areas with lots of colors and visual effects. Because who cares about art direction.
I wouldn't think you would need to have studied color theory to understand the significance of scene composition. One of the main reasons I loved Majora's Mask was due to the sheer atmosphere of it all, and a lot of it was owed to how drab and washed out the world seemed despite the area being far more vibrantly designed than OoT.
Yes, the N64 version's fog looked that way because of technical limitations. However, anyone who works in any form of artisitic media will tell you that working with technical limitations is just how you do things. You adapt when things won't work right. Very rarely do games look exactly like the concept artworks that spawn areas and ideas for them. To many, gray, drab and dreary is exactly what that particular sequence needed. Similarly, the late game color changes hugely exaggerate what was initially slightly more grounded.
One of the major projects I respect deeply is the
Resident Evil 4 HD texture project.. They've gone through great pains to assure that the textures are almost always a 100% match for color tone and don't change the scene's initial composition. It is a mark that most texture packs completely miss, and in some cases, remasterings such as this.
I am a fan of a lot of the visual changes and improvements, which has given this game a more modern look. I am highly anticipating trawling through the game again at a framerate that isn't sub-20. And perhaps it is because I am a very visually driven creative individual who invests a lot into mood and composition even when I'm simply writing out a short story, but some of these changes just alter the mood too much for my liking. I shouldn't have to be told I have "Nostalgia glasses" for that.
