I've been mulling the prequels over (AGAIN!) and trying to conciliate what's possible in editing/reshooting with what we know from the OT pre 1999, and I think I've come up with my most practical idea to date, whilst still keeping the reveal in ESB. It's a combination of existing ideas from myself and other members, most notably Bingowings' dissociative fugue concept - at least he's the first person I remember bringing this up.
Basically, when Obi Wan takes Anakin on as a student (Obi is not a student himself and Qui Gon, if he exists in said edit, is just a fellow Knight), we would have one of the council members make reference to Obi Wan's previous failed student. This could be done through filming new human council members (something the prequels sorely need) or alternatively through redubbing. They could elaborate and say the student turned to the dark side, but "failed" works also. This sets it up from the get go that Obi had an apprentice so we can immediately reference that line in ANH "Was a pupil of mine until he turned to evil" and assume it's this person.
Then when we meet Darth Maul, who either remains nameless or is called Darth VADER. It's revealed through redubbing or creative re-editing of existing dialogue that HE is the failed apprentice. Maul/Vader still kills Qui Gon, Obi still cuts him in half, but we get some kind of hint that he's not dead - whether it's shot of him dragging his torso away after his fall down the shaft or a full on rebuilding scene where you see him get some robot legs attached or even put in the Darth Vader suit. There are a lot of variables to consider and they all depend on resources available when shooting.
In the next film/s, Grievous would be scrapped in favour of Vader in full costume.
This is the point at which I'm not sure whether it's practical or doable, but Anakin would fight VADER. Footage of Anakin fighting (Dooku, Obi, droids, whoever) would have to be roto'd out and creatively superimposed into footage of costumed Vader swinging his saber (which would require the costumed actor to be fighting thin air).
Obviously, it would be really difficult to get them to appear to interact convincingly so you'd have to weigh up whether it would be better to just film a new Anakin actor (seeing as we're so limited by the Anakins we have anyway). That's more into the realms of a refilming rather than a re-edit with refilmed elements though, so I'll shut up about that for now.
In the Duel, Vader taunts Anakin with threats that after he's done with him, he'll kill his master and his loved ones. Anakin strikes Vader down in a rage.
He walks away.
The scene may get a bit 'visiony' like the 'force cave' in ESB. (or change in some way to make it seem surreal, like something isn't quite right)
Anakin turns just in time to see Vader rise up behind him and raise his saber.
We cut away to hear Anakin scream and then silence.
This is the point at which Anakin "dies" and "becomes" Vader, though the viewer doesn't know it at this point.
A first time viewer would think that Vader actually killed Anakin. A viewer who already knows will see it as a force-vision and an allegory all in one. Anakin, in giving into his hate, has taken up the mantle (and costume) of the Dark Lord.
From this point on, we see Vader committing atrocities in costume and no one need be any the wiser....