It was dumb having it at the end of ROTS anyway, and personally if you guys are going for a 6-part saga I think it would be best to drop the entire ending of ROTS and try to retain the 'I am your father' twist. i.e don't show Anakin becoming Vader or Padme giving birth. Just have them both 'die'. Of course, having Luke with the same surname as Anakin does make it a little hard to keep the surprise...
You could show just Luke being born and later after all the twist have been revealed, show the twins being born and Anakin become Vader.