I had another brainwave when it comes to Threepio.
In TPM we see TC-14 on the Trade Federation Ship.
If she was recoloured gold and given some of Anthony Daniels lines from the prequels or the Radio Drama you could create a different arc for him.
He starts off as a Trade Federation protocol droid, he is used as their translator (because they no longer speak Engrish... allowing for Magnoliafan style subtitles to make them into darker characters) he is given orders to encourage the Queen to sign the treaty and make sure that no harm comes to her until she does, he takes his duties so literally that he ends up being dragged onto the Queen's ship when she escapes.
True he would still need to be put into some of the footage but seeing as he never leaves the ship on Tatooine he would be in TPM and meet Artoo but not meet Owen.
At the end of TPM the Viceroy declares that it's too late to sign the treaty and because his primary mission no longer achievable Threepio continues to serve the Queen and try to ensure her safety.
He could be in the background during the Coruscant scenes in Episode II (but stay behind on Coruscant with her decoy so not lose his head on Geonosis) and encourage her to return to Naboo with Anakin, and he would be in the birth of the rebellion scenes when they are put back into ROTS.
Bail wipes his memory because he doesn't trust him (because of his past and because he has been around during the planning stages of the Rebellion).
That way he's in all of them and it sets up the droids are slaves theme continued in the OT.