For me it's the following:
- Physics not tied to framerate
- Widescreen
- Improvements from the 3DS version added (better models, animations, additional foliage and improved Water Temple)
- The 1.0 ROM specific features (Ganondorf's blood being red, blood being in the Shadow Temple and the Islamic Fire Temple theme)
- High-res textures
- More stuff in Hyrule Field
- Physics not tied to framerate
- Widescreen
- Improvements from the 3DS version added (better models, animations, additional foliage and improved Water Temple)
- The 1.0 ROM specific features (Ganondorf's blood being red, blood being in the Shadow Temple and the Islamic Fire Temple theme)
- High-res textures
- More stuff in Hyrule Field