That rotoscoping job on Anakin's saber was nicely done. I like the red saber, too, and, if Anakin were to construct a new saber or simply replace his saber's crystal with a red one between the time he massacres the Separatist leaders and the time Padme arrives on Mustafar, I think it would work well to explain some of the time that should pass while Padme journeys there.
I can imagine a sequence where Anakin metamorphosizes from emotionally-torn to resolute-Dark-Side-devotee; he'd mourn everything he had done recently like he does in the film, then march off into one of the volcanic crater's, think about tossing himself in, catch a glimpse of a shiny red jewel in the volcanic rock, touch it and have a Dark Side vision of saving Padme or of bringing peace to the galaxy with him as absolute ruler, replace his saber's crystal with the red one, then enter a trance as he waits for Padme to arrive.
But to try to actually create a sequence like that... whew! That'd take more talent and time than I've got.
Still doesn't explain the lightsaber Ben gives to Luke, though. Don't have that part figured out. If someone could cobble together some audio of Hayden Christiansen saying something like "Obi-wan, if anything should happen to me, give this to my son", then maybe something could be done. Then again, Anakin and Padme have been keeping their entire relationship a secret from Obi-Wan, though I think my edit may end up downplaying what Obi-Wan does and doesn't know significantly.
There was so much more of Anakin, Padme, and Obi-Wan's relationship that Lucas should've put on screen! Could've done it, too, probably by scrapping that whole pointless battle sequence on Kasshyk.