-I resequenced the Anakin/Obi-Wan talk leading up to the duel so that it flows like a real conversation. The music had to be changed to accomodate these edits, and I used some that felt appropriate to the scene. I'm not sure what music would accompany a final version, but it would be something along these lines.
-New music for the Yoda/Palpatine confrontation. This all comes from the Throne Room in RotJ, with a hint of the Force Theme for Yoda, and then of course a strong rendition of the Emperor's Theme when Palpatine zaps Yoda.
-I combined two sections of the Yoda/Palpatine fight here, as it seemed to flow much better this way. Deleted silly lines ("My little green friend," "And not short enough it was.") and silly shots (Yoda opening his eye). I left in the original music at the start of the duel b/c I couldn't find or think of anything to replace it, but that's definitely something that needs to be changed.
-I messed up trying to edit out Obi-Wan and Anakin's "hand hold," and now it appears as some missing frames. But that needs to go (too cheesy, IMO).
-In one of my favorite edits, I cut from them fighting by a console to much later in the duel when their sabers hit a control pannel turning off the "lava sheids." This cuts out some stupid stuff in the duel (the saber twirling, the super force push). We also lose the table-choke, which I like, but it doesn't really fit in the flow of the fight.
-The transition into "Duel of the Fates" starts because I wanted to sync up the crescendo of the piece with the wide shot of the Chancellor's podium rising in the senate. It also continues to work well with the rest of this part of the duel.
-I wanted to cut out some of Anakin and Obi-Wan's bridge-crossing (including the stupid flying droid), but I needed it to pad things out to sync up with DotF.
-Some resequenced shots now has Anakin's punch flows naturally. I have no idea why this was edited the way it was originally. (As an aside, I wish I could use some of the behind the scenes footage from the DVD with Anakin and Obi-Wan punching and kicking each other more. I don't know if it could be made to match the film footage though.) Another personal favorite edit is the big crescendo of DotF syncing up with Anakin and Obi-Wan grappling in front of the volcano.
-In RotS, DotF was present in this next section of the Yoda/Palpatine fight, but it felt cut-and-paste without anything syncing up. I've tried to make it flow better with the music. Also, in the big force lightning explosion, I've tried to make it look as if Palpatine overpowers Yoda and thinks he's won.
-When the crane falls into the lava I've overlayed ESB music b/c it syncs up well with the visuals. Not sure if it's the way to go for sure, but I like it better than the original.
-The Palpatine/Stormtrooper conversation has "Then he's no dead" edited out. This goes further to show that Palpatine thinks Yoda is dead (killed in a similar way to Mace).
-In the final section of my clip, I've come up with what I think its the best option regarding Anakin's injuries. Having him fall over the "waterfall" has its appeal, but then you lose the entire conversation with Obi-Wan. That's a must-have, IMO. But the lava surfing, the dialogue with it, and the eventual "You underestimate my power!" jump all leave much to be desired. Having Obi-Wan jump from the crane to the gound, and Anakin follow (resulting in his dismemberment), works very well, IMO. "Battle of the Heroes" carries this scene along, and the final two strong beats of the music accent Obi-Wan's chopping-up of Anakin, and transition well into the somber music to come.
So those were my thoughts on making these edits. Basically it was me just doing what I thought would best improve a mediocre sequence. A lot of stuff is sketchy, but this is the direction I'd take if I were to sit down and edit this "for real."