If Anakin knows that the Emperor has an unlimited supply of his own clones that he can transfer into at any time, then it would be one way that the Emperor was so powerful that Vader wouldn't just double cross him right off the bat. And after the whole badly damaged body thing, Vader would be wanting to learn the secret of the cloning and the body switching thing from him. Another reason not to kill him. But then these things get pushed back out of his mind for whatever reason and he stops thinking about trying to overthrow the Emperor until he meets Luke and finds someone else powerful enough to help him.
Anyways, that's not that important, but just how the "shaft scene" changes in this context. I think Vader's redemption is probably the best in all of the Star Wars trilogy and I would hate to introduce any new aspects that would lessen it. So, is Vader's moment less cool if he knows he is only buying a few moments of time for Luke and the Rebellion? If he knows that he has only set the Emperor back a little? He doesn't have the heart to tell Luke just how powerful the Emperor is?
Anyways... I like the idea that the Emperor is trying to achieve immortality in this unnatural way when the Jedi receive immortality just by being Jedi. I don't think it's quite put that way in any of the Dark Empire stories... but the subtext is kind of there.
Matt