Final cut? Great Googly Moogly!
Great points about the Han/Leia theme. I like the idea of taking the Ep III balcony music. My biggest fear around this point is that the work you do to fix the romance might get undermined by the score they chose for this. As long as you have options, I'm encouraged. I would argue that Han/Leia and Anakin/Padme are not that unalike. Han is a marked man and Leia is a Rebel leader-- their love is not forbidden, but just as doomed in ESB as these two are in SOTD. If there were only some alternate take, some variation on the theme that was vaguely recognizable instead of solidly linked to any major ESB events.
I can't help remembering what a lift it was in MagFan's "BOTF" to hear those ANH cues in the pod-race. Just a single quote of the Han/Leia theme placed carefully and discreetly could change the flavor of this whole movie-- making it more OT. But this is the last I'll speak of it because I can tell by your comments and ideas that you understand music better than I do.
Two last points to emphasize since the last cuts are being made: I love your outline but two points are unclear.
1. You say Anakin and Padme "disobey" Mace Windu when they run off to save Obi-Wan. If you cut Mace's direct order to stay on Tatooine, that gives them a loophole to sneak through so they (particularly Anakin) don't seem so immature.
2. In this cut, Anakin more or less blames Obi Wan for his mother's death. It isn't outright blame and there isn't solid logic behind this emotion -- but it is there and has to be processed.
As it stands, Anakin kills the sandpeople, yells about Obi Wan in the garage, buries his mom, then runs off to save Obi Wan.
When he finally gets face to face with Obi Wan, they pick up the "hilarious" banter they had at the beginning of the movie without a hint of residue from the death of Shmi. Obi Wan even seems to understand Padme better than Anakin when he notes that she "seems to be on top of things."
This stuff all seems incongruent. Where are Anakin's mixed emotions? They finally surface when Padme falls out of the gunship during the clone-war battle, but their banter during the "execution" really interrupts this thread.
Can you give Anakin a less jovial attitude to Obi Wan in the arena? Cut a couple of his lines? Christiansen's glares at McGregor seem to fit Anakin's mixed emotions better than his dialogue. Let his glares cover a couple of these "jokey" beats so that we remember Anakin's got a bone to pick with his master. Cut Obi-Wan's line about Padme and let it be part of Anakin and Padme's off-screen plans. After they kissed, we can presume they talked briefly about how they plan to escape.
On the Anakin lines you keep, the line readings you provide can contain more hints of something dark toward Obi Wan-- the reading of "We're here to rescue you, Master" can be almost threatening. That'll play off funnier when Obi Wan looks at his chains and says "Well you're doing a great job!"
The point of this is to let Obi Wan's talk with Anakin in the gun ship be a major story beat, when he asks "What would SHE do?" That's where Obi Wan and Anakin re-establish their friendship.
That's where Anakin finally is able to get his emotions into some kind of order. He knows Obi Wan never meant to let Shmi die, he just had his sights set on making Anakin a Jedi. At this moment, Anakin makes a Jedi-like decision to leave Padme and continue the mission. That's the key moment in this story-- the story of Anakin resenting his "Jedi" restrictions--breaking the rules--throwing aside his teachings--then finally picking up the mantle again. That backbone will turn this movie from mush into a story.
Then, if Anakin's "rushing into battle" against Dukoo can come off as smart rather than suicidally stupid, I think the Anakin story in Ep II will finally be complete.
If, on the other hand, you don't address his mixed emotions to Obi Wan when they first see each other again in the Arena, the entire throughline of Anakin's story will lose focus and limp to the finish line as it does in the AOTC cut.
The choice is yours, Jedi. Do or do not. There is no try.