Ok, now I see it. By the rule of two, either Vader or the Emperor has to die for Luke to become a sith. They wouldn't want to let each other know that they are planning to replace them with Luke, so they wouldn't work together.

Still, in Empire, Vader wants to persuade Luke to rule with him as father and son, which implies that he wants to get rid of the Emperor. If you'd want to change the prequels so that Vader's turn against the Emperor is not hinted at, you'd have to change Empire, too.