For those of us who loved the OT and want to keep it sacred, but would also like to see a version of the Star Wars saga that is completely integrated with all six episodes, I think that a process like that would be ideal to keep you connected with the character of Anakin.
Maybe it'll be easier to visualize after seeing Episode III, but right now the thing that makes it hardest for me to reconcile Anakin/Hayden as Vader is the English accent or whatever JEJ was going for. It was of course great for the originals, but when watching them all as one movie, I'd really like to have that connection, even a very subtle connection to the image of Anakin in my mind when watching Darth Vader. Just a slight hint of the man he used to be.
Then again, I also wouldn't be opposed (if done well) to putting Hayden in prosthetics and reshooting the Vader unmasked scene at the end of ROTJ, eliminating Shaw completely. Again, Shaw's English accent, barely noticable, but still. I think it would make the "saga edition" more complete. The originals are fine on their own.
By the way, HS vs. IJ, where did you hear this? Last I heard Lucas was reported as saying everything is the "way he wants it now", and no changes would be made to future DVD releases, which I don't believe, but as far as I know, it's the "official" stance they're taking right now.