Having done some more research into this as well as the 2004 DVD releases, it seems that the issue with the color palette on the DVD release could very well continue to be an issue on the blu-ray, as it seems that George Lucas personally oversaw the remastering process that the DVD used -- and it seems that the blu-rays are using them unless otherwise stated. The blu-ray trailer does depict the same messed up lightsabers in Return of the Jedi that the DVD had. Here's a rush job getting captures of how it looks in the BD trailer, and how it SHOULD look from the original release (hidden behind spoiler because it breaks the frame and I'm too lazy to resize):
Click here to see the hidden message (It might contain spoilers)
If the video is properly mastered from the source, the black "slug" on the Emperor should be removed as well. It's my understanding -- and I didn't personally see it -- that it simply wasn't present in the original theatrical release of Return of the Jedi as it was matted to the coloration of the film, and the conversion to home video is what resulted in its appearance.
As for the remastering of The Phantom Menace, it was necessary to insert digital Yoda.
Edit: It seems that the remastering done for the 2004 DVD release actually does improve colors quite a bit, but the process itself is the cause of the lightsaber gaffes and some weird coloring in scenes where it isn't appropriate.