From what I'm hearing there will be a special edition of TPM and AOTC (Yoda CG)...
I think if there should be one major change to AOTC, it should be the score. Due to last minute editing, the music is just sloppily cut and pasted all over the film as well as being complimented by the TPM soundtrack during the arena battle.
I think I read that JW was really disappointed with the way the score turned out in AOTC, I think therefore it should be redone or re-edited...
The droid factory and the arena sequences being the greatest offenders.