I really like a lot of your re-ordering of the two films there Bingowings, especially the link between the two films and the creation of the clone army. And adding Dooku in as a Jedi in the first film; would be great to see him on the council. I also wonder if it would be possible to give Yoda a bigger role in TPM, maybe even re-instate him as Obi-Wan's master, and just have Qui-Gon and Obi being Jedi? I would make a couple of suggestions; for the title crawl I would suggest two things. Remeber the power source idea? Essentially the crawl would include information along these lines; the Naboo have recently invented a revolutionary power source which will allow the creation of super-sized ships and battle stations. Following this the King and Queen of Naboo were assassinated leaving their young daughter as queen. Various Galactic powers are vying for control. The next suggestion would be moving up the Gungan's battle to the middle of the film, given they just loose, you could stream line the end of the film to remove it's overcomplicated ending even more buy using the Gungans loosing to show the people's suffering. (Possibly also interspace with a few sceens from Terminator 4 with droids rounding people up). 

The reason I really like the power source idea is it paves the way for the Death Star and Imperial fleet, and also gives a good reason for wanting to control the planet...

I really really do like your re-ordering of AotC; though I have to say I'm not a fan of Dooku just being a fallen Jedi. Prefer him as a Sith Lord, would want to keep the Force fight between him and Yoda but scrap Yoda jumping around loads. Would also want to see Grevious introduced towards the end AotC killing a few Jedi personally.

Also for AotC, the title crawl could say that having turned Naboo into a democracy and abolished the monarchy Padme was voted Naboo's senator. I think that adds to her being the exact opposite of Palpatine/the Emporer....

My 2 cents