Perhaps you'd have Anakin acting as a renegade Jedi wearing armour not dissimilar to Vader's eventual setup. That way, Vader simply slips into lifesupporting armour based on his look rather than be given it for no apparent reason when he is beaten by Obi-Wan. Since GL swung the emphasis onto Anakin/Vader, then make Vader a bigger part of the myth, as if he is a separate character and push the suspicion off him until ESB. That way Obi-Wan could fight Vader as he implies in ANH and right at the end, when Vader is beaten you could have him revert to Anakin for a brief moment that allows Obi-Wan to discover who he is...?

I do agree that you should have Anakin's story, but have it not so projected as it was throughout the PT...it was almost like 'here's a good boy, wanting nothing and giving everything. But wait, he's exhibiting signs of darkness and he's starting to wear dark clothing so he must be a bad person now.' You need to have a certain amount of ambiguity to tie up enough with the original trilogy and the revelations it reveals.