When Obi-Wan is saying goodbye to Anakin for the last time it would be a good place to insert a line saying something like "Of all my students you were the best" (only better) which would imply that there had been others since.
As for Hayden's acting making more sense if he has a split personality, sadly that only remotely makes sense if it happened before Episode II.
The smirks he gives Padme and the tantrums seem to point to an already unhinged actor...erm...character though some of the vacant expressions could be called on.
Re-dubbing his lines still seems like the surest way for me to get the most out of any reworking of his character, even this one.
It would be interesting to have cut away from Shmi's death and later extend the massacre of the Tuskens by a hooded or masked character and not have Anakin admit to it.
That way both things happened but the massacre is the first atrocity of Anakin's shadow self Darth Vader.
If you cut the Sith naming ceremony and have Mace dispatched by some equally shadowy figure it could also obscure the truth.
Grievous is known to take a particular interest in killing Jedi but what if some of that is actual Vader's actions being attributed to Grievous?
It would tie in with what Lucas said back in 1977:
George Lucas said
“When the Jedi tried to restore order, Darth Vader was still one of the Jedi. What he would do is catch the Jedi off-guard and, using his knowledge of the Force, he would kill the Jedi without them realizing what was happening. They trusted him and they didn't realize he was the murderer who was decimating their ranks. At the height of the Jedi, there were several hundred thousand. At the time of the Rebellion, most of them were killed. The Emperor had some strong forces rally behind him, as well, in terms of the army and the Imperial forces that he'd been building up secretly. The Jedi were so outnumbered that they fled and were tracked down. They tried to regroup, but they were eventually massacred by one of the special elite forces led by Darth Vader. Eventually, only a few, including Ben and Luke's father, were left. Luke's father is named Annikin.”
For a time the good Anakin and the evil Darth Vader exist in the same body as a split personality but eventually Vader overwhelms the good persona, which is a handy way of getting around how he can murder children in one scene and be fearful for the life of his own child and his wife in another.
Then the problem boils down to the duel with Ben.
It's an epic duel (though it could do with some trimming) but would anyone be brave enough to dump most of it for the sake of keeping the surprise in ESB?
I did suggest obscuring Anakin's face behind a mask but that would be basically a reshoot.
You'd have to mask off all of Hayden's moves and replace him with a shadowy figure and remove all trace of Anakin from Vader's mechanical re-birth.
Clearly if someone were to attempt this angle it would need a lot of thought and a lot of discussion and a lot of hard work.