One thing that irked me is the visuals in 64 3D can be inconsistent.
The ending sequence in particular looked rushed. The shot of the Great Fox flying back to Corneria showed a really ugly looking/textured planet, while there are several other versions of the planet shown earlier in the game which looked much better.
And the very ending 'sunset' scene, no attempt was made to add 3D effects to the clouds, or to adjust the lighting as the Great Fox surged into the frame. Infact, the background was just a flat image/placeholder.
Otherwise, the game looks great.