One possibility that just popped into my mind is what if Anakin had some sort of split personality (that he was being both Vader and Anakin at the same time).
We could see some of the crimes of Vader being committed by a shadowy hooded character (some of these could even be acts done by Grievous in the original cut).
All the while Anakin is getting nightmares about Padme being killed and being lured along by Palpatine while these vile acts are being done by this mysterious stranger (possibly out of sequence with the events as we saw them in the cinema).
The murder of Younglings could happen at any time (some mysterious agent sneaking into the temple).
The idea being that the death of his mother drove him insane and he only remembers these deeds when it's too late to go back.
Possibly bonkers but just thought I'd share it.