My updated ‘Superweapon’ plot for Episode II:
Geonosis; the Republic’s dumping grounds.
(Remember to turn on sound!)
https://gfycat.com/JaggedBrokenHyena
After some unknown battle, a Republic fleet dumps a Federation Battleship onto the largest scrap heap known in the Galaxy; Geonosis. Little does the Republic know that this planet is the headquarters of a vast rebel alliance, known as the Separatist Union. Plotting their first course of action, the Separatists devise a weapon so terrible that their victory over the tyrannical Republic is assured.
(Remember to turn on sound!)
https://gfycat.com/GroundedGivingBluetonguelizard
The rest of the plot would remain relatively intact. Amidala’s assassination attempts(s) would happen as normal, except the dart mystery would lead Obi-Wan to a find the dart registered to a man named ‘Fett’, living alone in a Republic Army training center on Kamino. He fights Fett in the rain and places a tracking device on his ship.
Obi-Wan would discover Geonosis and the next time we see him, at the start of Act III, he’s captured and interrogated by Count Dooku, who explains that the Republic is a truly corrupt power under the control of Darth Sidious.
After the Colosseum battle, a voice comes over the radio on a Republic transport explaining that Dooku is carrying the plans to a superweapon. Obi-Wan and Anakin make chase, climaxing in a duel. Unfortunately, however, Dooku escapes with the plans, leading to a total Galactic Civil War.
Anakin’s story wouldn’t really be changed as drastically. Anakin would start out as a noble Jedi Knight who feels like he’s ready for anything. His love of Padme isn’t ‘forbidden’ and his overtly creepy moments would be cut.