This ^ is very exciting work! Not just switching up a couple of scenes but skillfully weaving seemingly disperate elements together in a bold new and cohesive way. Awesome job. Even in this rough demonstration I can see how everything is going to flow beautifully. You've got me hooked on this project now.
Couple of points...
The suitcase scene ranks as one of the worst in AOTC (Stiff competion I know) so I perhaps wouldn't open with it. However it's mericifully brief in your edit. There is nothing that can't be covered in the crawl. The next scene in the Theed palace has more of a spark.
You could also open with Obi-Wan listening in on Dooku's plan, then cut to Padme talking with the Queen on Naboo. Just an option.
After the geonosis opening are you going to move to the assassination/bombing on Coruscant? and is Padme going to be pro-army in this edit? You could recut this scene to have her proposing an Army after witnessing what Dooku is up to on Geonosis...