If its okay I’ll just start splurging ideas out that may or may not be appropriate to your edit! But just sort of radical enough to maybe fit your approach to editing. They also assume we don’t have a TPM necessarily.
I always liked the idea of giving him a mask - like Darth Revan/Kylo Ren. This would be with the intention of him un-masking just before the Obi-Wan duel, to add more weight to the fight.
Through the magic of science, what if it was possible to swap the heads of Qui-Gon and Obi-Wan in the balcony scene in TPM (ie the “Master you’d be on the council right now…” scene) with Dooku and bearded Obi-Wan to an earlier point in the film.
Remove YODA from the film entirely - he’s just referenced heavily. During the Dooku/Obi-wan duel, take the dialog from the interrogation scene, but swap the Qui-Gon references to Yoda (“I wish YODA was here right now, I could use his help” etc). I always felt the interrogation scene was quite flat, as was the duel, so maybe the dialog mixed into the duel could add some weight again. “You must join with ME Obi-Wan” right before a scene change mid fight would be great.
Are you doing SITH dooku or rogue Jedi Knight dooku?
If you lose TPM, you have the potential for Droids to invade NABOO.
An opening could be having the Battle of Naboo, with Padme leading a fight to the hangar to get to coruscant. You’d obviously lose the potential to return to Naboo later in the movie though…
Alternatively the invasion of NABOO could be a motive for Anakin and Padme leaving?
If you really wanted to turn the film on its head - could Anakin and Padme be from Naboo? Could the film open with the romance scenes on Naboo? And instead of travelling from Coruscant to Naboo its the other way around - theres alot of walking/talking that could be leading TO transports and not away from them
REUSED FOOTAGE -
I skipped through a film called VIRGIN TERRITORY the other week, thinking a medieval film with Hayden could be a great source for Anakin stuff. I’m not sure it is - he has this weird fake british accent in it - he does however do alot of gardening though, which might some how fit with the scenes at her parents house? (could he be a family friend?)
This probably wouldn’t work - but I did wonder once if anything from the outtakes could actually work in an edit, you actually see more chemistry between Portman and Hayden off screen. There’s the odd apologetic laugh and hug that might make them believable - just in the totally wrong parts of the film.