ultimatefan,
I figured out my issues with the transfer of the DVD. It's a combination of alot of things. It's the Genesis digital camera. It's Sigel's lighting scheme and the intented look of the film to feel retro, while being new, and replicating the soft look that Donner's Superman The Movie had.
The issue with the noise sprang up on the Episode II Attack of the Clones DVD and like Superman Returns, it was mostly during the dark, nighttime scenes. With that film, Lucas was using Sony's first generation digital camera. On Episode III Revenge of the Sith with 2nd generation cameras, the issue of noise during dark scenes and shadows was completely gone.
Again, during daytime scenes and scenes that have a mixture of light and shadow, the film looks fantastic. The grain (digital noise) is part on purpose it seems and part an issue with the camera. It's hard for compression artists to do these direct from it's digital source transfers on DVD.
Again, very curious about the HD version of this transfer.