Well, this one pits my favourite movie of the saga against the one I genuienly despise. Sorry, I had to stop halfway in, I really hate "episode 2" so much. I didn't notice any major technical issues, but while this is an interesting concept, it doesn't really work for me. Why? Because the two movies are simply nothing alike. While one throws you right into one brainless action sequence after another, the other one starts slowly, to carefully introduce its characters at first. As a result, I was annoyed when episode 2 showed up, and Star Wars then almost bored me, which is just sad.
Regarding your musical additions, I mostly liked those. You managed to pick the right music for its respective scenes and it felt quite refreshing. The title text-screens i didn't like that much, but that may be because I am simply not able to accept an alternative to good ol' SW crawly :)
I did however watch the prologue feature on the second disc and I liked it. There were some nice choices there, I especially liked the use of Ian McDiarmid's naration. The narative of the prologue felt alright, maybe slightly all over the place at times, it could benefit from some more trimming, but overall, I liked it much more then the main feature.
Sorry for the criticism, I really hope you continue to make fanedits, as I said, this was an interesting experiment, the bad thing with experiments is, however, that you just can't please everyone :)