It was a deliberate move on Lucasfilm´s account to color saturate the new 2004 DVD´s to make them look more like the PT films, which have much more contrast, are more colorful and with deeper black levels. You can see that those 2004 SE DVD´s are not closer to the original vision by Lucas back in the 70´s and 80´s then the LD and VHS releases. I remember clearly when seeing the movies in the cinema back then (and also in 97) that they had this desaturated gritty look that is represented quite well on the LD transfers. Lucas is making changes. He´s not only adding CGI, changing the story and characters, but he is also deliberately changing the way the films look, he wants a more "cartooney" look obviously because that´s what he´s brought us this time.