My personal take on a separate Anakin and Vader playing out in the prequels would go down what I would have assumed the obvious route of a clone Anakin being involved and becoming Darth Vader. I always assumed The Clone Wars would be over the issue of cloning, not a reference to the composition of the armed forces that fought the war. Since when has any war been named for the soldiers rather than the nature of the conflict?

In any event, a clone Anakin would make everything said in Star Wars true. He would at once be both Darth Vader and the good friend of Ben Kenobi who was betrayed and murdered by Darth Vader. None of this mamby-pamby stuff about being destroyed by Vader simply by becoming Vader. Lot of interesting plot points could result, with the audience in the dark about identities when best for the story, and aware of who-is-who when that suits the story. Which one comes under the thumb of the Emperor? Which one duels with Ben Kenobi? Which one sleeps with Padme Amidala and sires twins?

It would itself be in the classic sci-fi mold of the evil twin (employed to great effect by Star Trek, Farscape, dozens of others). Best of all, there could be a mirror twist ending to the prequels where the audience finds out Darth Vader is NOT Luke's father.

Of course, then the series could never be watched 1 through 6 (thank goodness), but it would be nice to have a big a kick in the guts surprise in the prequel trilogy as there was in the first, and the handy gimmick of the Clone Wars provides the obvious way to have the second surprise be a neat reverse of the first.

And, heheh, Ben Kenobi would go back to being the truthteller he was always meant to be.