Secondly...I was trying to only use thematic references sparingly. For example I used Duel of the Fates once in TPM instead of echoing it over and over again. This was a lot harder to do in the OT because themes are echoed OVER and OVER.
Ultimately...the OT has more memorable cues and certainly more (and better) concert suites. Leia's Theme, Imperial March, Yoda's Theme, Parade of the Ewoks, Luke and Leia's theme, and the Forest battle are presented uncut and make up the bulk of the time difference. Across the Stars is basically split in two with a little bit missing from the middle, I think...Duel of the Fates was trimmed because I find the stop/start nature of that concert suite annoying as all get out. Battle of the Heroes is only missing the very beginning because the edit worked so nicely with "Enter Lord Vader". Anakin's theme is also presented uncut.
If I had the same quality and quantity of concert suites...the PT disc would be longer. I wanted to add the Flag Parade...but couldn't find the right place for it...and it seemed to detract from the story.
The prequel disc will be re-edited when full scores are available for each.
As far as flow...I don't think you've listened to it yet...right?
The PT disc is much better than the OT because the scores were so much harder to edit because Williams was working with a locked film and transitions were hard to get around, whereas the PT films were given a much more open-ended feeling that allowed me to cut more effectively.
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As for LOTR...that's a good idea...but the score certainly doesn't speak to me as much.