Bingowings said:

It would be easier to have Qui-Gon suggest to the council that Vader is already sufficiently trained when Kenobi decides to take on Anakin as his pupil (using the lines directed at Obi-Wan). You could maybe add a shot of a youth either screwing his face up because of being put out by the new arrival or filling with hubris from this swift promotion to Knight.

Either way could lead to the Dark Side.

The slaying of the Tuskens, assassinations of Jedi (currently done by Grievous and the clones following order 66666666) and the Raid on the Temple could then be done by Darth Vader in Anakin's nightmares.

We could see Anakin rush to the Chancellor from Mace (who is genuinely acting above his authority despite being right about the courts being rigged). We could then assume Anakin is killed when Palpatine changes and starts throwing lightening around.

The Anakin/Kenobi duel could edit all visible references to Anakin down to a red saber and Obi-wan narrowly defeating an unseen former pupil.

If the viewer believes the emperor to have killed Anakin, that will undermine the whole "former pupil betraying your father" thing so we'll know something is up as soon as Ben says this blatant lie. Having said this, I love your idea of Qui Gon suggesting Obi's existing apprentice is ready when he takes on Anakin.

I feel the dissociative fugue idea only works if it's after Anakin's "death", so more like a metaphorical possession when he kills the original Darth i.e. the torch is passed. To have it happen in a 'Tyler Durden' way while the audience is still under the impression he's alive/a good person is a bit of a cop out IMO.