I honestly feel like the 3D version of the game is inferior to the original.
The dramatic increase in brightness and color saturation damaged a lot of the atmosphere the game had. Just compare the final battle with Ganon in both versions to see what I'm talking about. Also, Link being the only character model they bothered to update was very jarring and hurt the overall aesthetic.
If you look at the original art you can see that OoT3D is actually a lot closer to the intended art style (which was very colorful and almost Disney-like). Miyamoto described the N64 hardware as incredibly limiting and they struggled just to get the wire frame models working. Young Link's hideous original model is all the evidence you need that the game was severely held back by technical limitations... I wouldn't judge the N64 version as a real indication of what the devs
wanted the game to look like.
There are times when the fog and drab palette actually served the game well, like the forest temple. It's a little too clear on 3DS, which makes it seem emptier. I agree that the Ganon battle is another example of OoT3D dropping the ball.
But you have to consider just how much of the content looks better-
stupifyingly better. It wouldn't make sense to play through 99% of the game with worse visuals just to get slightly better visuals the other 1% of the time. Also, every model in the game was updated, not just Link. Link's is just one of the few that was
dramatically different.
I do wish they had adhered to the concept art with the same dedication for Majora's Mask. They kind of phoned it in and reused the same assets and style from OoT3D, even though the art for MM was dramatically darker and more heavily shadowed. I would have loved to have seen these guys actually look like this:
While almost everyone agrees about Hyrule field being empty and uninteresting, you gotta understand what that landscape was for a lot of people back in 1998.
The original field being boring is understandable, the real problem is that they didn't fix it at all in OoT3D. They added in a few little flowers here and there, otherwise it's the same old empty shit. They could have added in more enemies like the wolves for rupee farming, or at least added in some more vegetation and tree types to diversify it more.
Majora's Mask avoided this problem by making Termina field a lot fuller and more dynamic. I'm not ever nearly as bored traveling around it, not to mention the Goron rolling and bunny hood help a lot.