Looks improved in the same way the Silent Hill games were improved.
Fog, the forgotten art.
This is a very ridiculous comment.
The fog in Silent Hill served much more purpose in Silent Hill. It's a horror game and the thick fog makes it hard to see what might be lurking around, which heightens the sense of fear. The fog in that cutscene in Majora's Mask is mainly there because that forest is a very small room where the walls are a flat picture of trees. If it were any less foggy that scene would look horrible. You can already see the edge where the wall of trees is.
In Silent Hill HD Collection they just reduced the fog and fucked up the fog effects. This made it possible to see things you weren't supposed to see. The fog had a very clear and unnatural fog line and fog particles popped in.
In Majora's Mask 3D they completely remodeled the entire scene. The trees are no longer a wall with a flat picture of trees on it. All of those trees are there (or at least 2D versions of trees for those in the background) as you can see thanks to the parallax.
See here you can see that the background trees have no parallax in the N64 version because they are a flat picture. You can see the border where the wall meets the ground.
The fog in the MM3D version of the scene also looks a lot more natural along with the light filtering through the trees and the shifting shadows from the supposed foliage making the scene a bit eerier. It has less fog because it doesn't need the fog like the original scene does, but the fog it does have is much more well-done.
Silent Hill HD Collection also fucked things up by retexturing the environment in a way that made everything look cleaner and less detailed, while MM3D's new textures improve the visuals completely.