MTHaslett said:

But how does Vader betray and Murder Skywalker? With the footage that exists? Who in the cast could become Skywalker?

If Darth Maul was Vader, and Skywalker was Qui Gon? ...No.

The only things that I think would work with the footage available (and I'm not saying I like any of these ideas) are either Anakin is Vader and Dooku is Anakin, Palpatine is Vader and Anakin is Anakin and we assume his actions lead to Obi Wan killing Anakin and 'Vader' (Palpatine) being responsible, or Obi Wan is Vader and he kills Anakin by removing the part where he is saved. Out of the three the last seems most manageable, but then you have Obi Wan and Vader's fight in E4 not making much sense at all.