Basically I'm thinking in terms of, instead of changing the "Obi-Wan once thought as you do" line (to something like "Padme once thought..."), we could make the duel fit with the line. Obi-Wan should be on the defensive the whole time, reaching out to Anakin. He's torn throughout the whole duel. Remove any indication that Obi-Wan has made up his mind as to what he will do. Think "The Searchers," when you aren't sure what John Wayne will do when he finally gets to Debbie. That's kind of what it would be like. As it is, the more I see it, the more sure of himself he seems, and then when Obi-Wan says "Don't try it," it seems rather schizophrenic. So keep out any decisiveness. It's not until he leaves the cliff that he finally makes his choice.
It might be a bit of a special effects challenge, but for starters, cut out the "Only a Sith deals an absolutes. I will do what I must." shot, including Obi-Wan igniting his saber. I don't have any details on dialogue, but make Anakin say something instead of "You will try." Then, in the shot where Anakin jumps, erase Obi-Wan's saber, and if possible (adywan...?), make it so he isn't in a fighting stance. So, Anakin's starting the fight here.
Throughout the duel, make Obi-Wan more defensive: for instance, cut the shot where Obi-Wan nearly stabs Anakin on the table.
Now, when they get across and the lava starts exploding, there are some shots where Obi-Wan and Anakin's faces can't be seen. If we can find a good Ewan McGregor impersonator, and Trooperman's dubbing Anakin, then I'll be really excited. Have Obi-Wan reaching out to Anakin, perhaps all the way through the swinging part.
Then, when we get to the irrelevant dialogue ("I should have known the Jedi were plotting to take over!" "Anakin, Chancellor Palpatine is evil!" "From my point of view the Jedi are evil!" "Then you are lost!" Ummm...what just happened here?) I'm thinking change it some, to something along the lines of this:
ANAKIN
I should have known the Dark Side had the true power!
OBI-WAN
Anakin, Chancellor Palpatine is evil!
ANAKIN
The Jedi are evil!
I'm not sure what to go with next. Obi-Wan's saying "You are lost!" seems pretty decisive, but I don't know what to make him say instead.
Then when Obi-Wan jumps off to the cliff, it goes something like this:
OBI-WAN
It's over, Anakin!
CUT TO: Anakin
OBI-WAN (cont., pleading emphatically)
Come with me, please!
Anakin is silent, and Obi-Wan begins to see what he's planning.
OBI-WAN
Don't try it.
This way, it's a much smoother progression. In the first line, he's trying to cut off the fighting. In the second, he's pouring everything he's got into this plea. And then he sees what's happening, and he's crestfallen, slowly realizing what he would do, and begs once, more, quietly, for him not to jump. But he does. Anakin's silence (a la ADigitalMan's cut) is now much deeper and heavier. With a lot of these changes, so much of the body language and silence will be much more meaningful.
And then I'm thinking it might be good to cut Obi-Wan's bawling Anakin out, but I'm not sure. It could also come across as Obi-Wan finally venting from all of the strain. Another possibility is to change the dialogue, perhaps omitting the frames where he is seen talking, but I'm not sure where to go with it, exactly.
So, the dialogue is pretty hazy for me. I'd have to think about it, and any of the more experienced dialogue writers around here can take a stab at it. Some altering of the conversation between Anakin and Obi-Wan before the duel might be in order. It always struck me as odd that that whole time, not once did Obi-Wan even try to ask Anakin what was happening, why he was doing what he was doing. If we can even approach fixing that, it would be a big help, but just for him to reach out to Anakin would be much more satisfying. If anyone can do Obi-Wan's voice, this could be really awesome, and be a big help in improving ROTS.