TPM: Replace the puppet Yoda with CG Yoda (which has been confirmed that they have done).
AOTC: Restore the scenes in Padme's parents' house, as they not only add depth to the overall story of AOTC, but they also strengthen Padme's story, the love story, not to mention they let you know who the hell that man and woman are at Padme's funeral in ROTS!
ROTS: Restore scene of Yoda landing on Dagobah and restore all of the Rebel Alliance scenes. (Rick McCallum hinted around at the Dagobah scene being restored)