Although I am not personally a fan of Hayden at the end (personal opinion only, not an attack on anyone else's opinion). The reasoning put out there at the time was that Anakin - the Jedi - died a long time ago, during Revenge of the Sith. His body was alive in the form of Vader for a long time after that. So when the body passed away the spirit of Anakin from the time of his death carried over.
It's a stretch I suppose, but one I can live with.
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