I posted this on the Revisited thread the other day, but its really probably more appropriate here. Its a bunch of ideas sort of mulched together in what could become an edit which cannibalizes footage from both Episode 1 and 2.

The film would open with Seperatist invasion of Naboo (The first act of the Clone Wars). Naboo and Geonosis are combined as a desert world, so Theed would be like an oasis city. The Geonosians are the savage desert dwellers who hate the Oasis folk. Padme is introduced fighting her way from the throne room to the hangar. Royal Starship escapes and blasts into Hyperspace.

Obi-wan Kenobi is introduced inspecting the Clone Army. Not sure what the plot hook would be for this, but for whatever the reason he meets and fights the Mandalorian. He pursues him to Coruscant.

Padme would push for the creation of a Clone Army to liberate her homeworld.

Obi Wan - following the Mandalorian - somehow gets tipped off that Padme is the next target. He sees an exchange with Zam and pursues them. Somehow he ends up on that droid thing and gets shot off. He falls and gets caught by a speeder - introducing Anakin Skywalker. Zam could be chasing them, but her speeder could have guns on it? The droid thing meanwhile arrives at padme's. The Jedi arrive just in time, Anakin meets Padme for the first time.

Anakin is charged with protecting Padme, Obi-Wan is charged with travelling to Desert-Naboo, and negotiating with the Seperatists.

Naboo as seen in AOTC becomes Alderan, a green peaceful world. Padme is revealed by a mysterious spy (using Darth Maul footage) Droids invade forcing them to leave.

Anakin takes her to his homeworld - Tatooine. The spy follows them there, hunting Padme by sending those ball droids looking for her. They recieve a message from occupied Desert-Naboo informing them that Obi-Wan Kenobi is to be executed (as an act of war). Padme, sick of running, decides that they should attempt a hopeless rescue.

They travel to Desert/Naboo (ie geonosis). There are no Droid Factories, just a massive occupying force. They are captured and sentenced to death in the arena. The Clones show up, and defeat the droids.

I always liked the idea of Dooku wearing a CG Mask until a big reveal moment. This would allow for an extra to stand in for him in some essential earlier scenes, as well as some easy redubbing with a mechanical voice.