Also I'm catching up with this topic bit by bit and just don't understand some people saying "it's fine not having an alternative apprentice as long as you don't explicitly state Anakin's surname is Skywalker". Now whilst I understand where you're coming from and that you believe a first time viewer would think that Anakin (Hayden) in the PT was Vader due to the fact he was:
Obi Wan's old apprentice
Seduced by the dark side of the force
That he hunted down and destroyed the jedi knights
Betrayed and murdered Luke's Father
And from that alone we might assume that Luke's father is someone we've never met who Anakin/Vader murdered.
However in the very same conversation, Obi Wan says Luke's father is
A Jedi Knight
A cunning warrior
In the clone wars with him dragged on an idealistic crusade
the best starfighter in the galaxy
And a good friend
.....and yet we've never met him. Why wouldn't we have met him? In fact the only person we've met that matches that description will have been Anakin, who Obi Wan more or less explicitly states became Darth Vader.
It makes it all fall apart because there's no alternative person you can connect either character to. Both descriptions point to Hayden in the PT. There should be some kind of ambiguity but there isn't any because there's no other prominent friend of Obi Wan that matches these descriptions for us to think might be Luke's Father - just the same guy again that fell to the Dark Side.
And if Ady was to go the other direction and we never SEE Anakin fall to the dark side in the edit and he just mysteriously dies off screen, we're left with the opposite problem then - why did we never meet this Darth Vader if he was a pupil of Obi Wan's? Why wasn't he ever mentioned?
This is why I think that, at the very least, we need the Jedi Killings by Darth Vader to be attributed to Obi Wan's old apprentice. Even if Obi Wan HAVING a previous apprentice that he suspects in the killings is only alluded to in redubbed conversations. I have no idea how this could be accomplished though. There's much more scope in getting some meaningful visual indicators of a seemingly "bad" apprentice by relegating Hayden Christensen to the role as he gives filthy looks throughout most of the saga anyway :p The ridiculous direction George gave his acting (act evil because you're going to become Darth Vader) would actually have a payoff then in a very effective The Usual Suspects, kind of way. The actual Darth Vader is the one we least suspected - Anakin. The kindhearted great Jedi IS Kaizer Soze.
I appreciate that this may be beyond the scope of the edit, but I've been thinking about this for so many years and it's the only way I can see of fixing everything. Unless you can find convincing ways of alluding to an old apprentice of Obi Wan's (whom we never meet) having turned to the dark side, I don't see how else the lines from ANH can be made to work with the Prequels.
There's also the superficial continuity-loving side of me that wants an Anakin that looks like Sebastian Shaw :)