"When I left you, I was but the learner"
Do you think that when Vader said that, he meant when he went to Naboo with Padme to marry? If so I think that would be great, otherwise if they are still together at the start of EpIII, that sets the story back quite far, because that means he has to leave him in the film and then start training as a sith.
Whereas if he's already gone, he could have been practicing his own skills in the 2-3 years between Eps II and III. Then it could open with Obi-Wan looking for Ani, when he meets Padme who is pregnant, she could tell him Anakin has gone, that means Anakin wouldn't know she is expecting, then she goes to Coruscant with Obi-Wan and the adventure starts there.
Who thinks that's what will happen?