This is a very fascinating concept. However, I think having him face Vader may be too on the nose. Could Vader be replaced with a shadowy-hooded figure that the audience could interpret as Sidious? I am not personally sure, but I really like the idea of Anakin confronting some form of a “demon.”
I definitely see where you’re coming from, as for first time audiences it could be interpreted as Anakin facing Sidious (as the prophecy says) and being killed. Either that or its interpreted as Anakin facing his dark side.
My idea was that I’d be a visual metaphor for the conflict between Anakin and Vader. Anakin, the passionate heroic Jedi, and Vader, the cold cruel Sith. A big goal is to make them feel like the same person by making Anakin colder when he’s using the dark side (scenes of him whining and complaining are gone), thus highlighting their duality (he seems so much more alive when he’s on the light side then the dark). And Anakin, through his passion for saving people, will be destroyed by his lust for power, the cold, mechanical Vader.
So in that sense, if you did replace Vader with a more mysterious figure, it would still work if that figure is entirely stoic, still, and cold. Because the point is that it symbolizes the duality between his passion and cold.