IMHO, the prequels should have been set THOUSANDS of years before the OT. Completely original story and characters in the same universe as the OT. If any of you have played Knights of the Old Republic, you know what I'm talking about. This would avoid all problems with continuity and visual anachronisms.
In TPM, Darth Maul says, "At last we will have our revenge [on the Jedi]". What is he talking about? No one knows - this is a complete nonsense line within the context of the films. The prequels should have been about THAT.