How would you "improve" the Star Wars Prequel Trilogy?

[Soundwave]

Episode I Alone:

- Federation (Bad Guys) Vs. Galactic Republic (Good Guys)

- Anakin is 14-years-old to start the film, not 9. He's a slave who races in pod races controlled by local crime bosses. He lives a very hard life, not knowing where his next meal will come from, trying to scrounge enough to help his ill mother. He doesn't live in a cozy Flintstones hut. He's a good kid, he helps out other homeless slaves and tries to use his pod earnings to feed as many of them as possible. Poverty is rife on Tatooine. His mom dies leaving him orphaned, Obi-Wan feeling sorry for him agrees to take him to Coruscant and the Jedi temple at least. 

- As much as I like Qui-Gon, I think I'd axe his character or kill him off earlier in Phantom Menace. This forces Obi-Wan to become the lead character and creates an immediate narrative between Obi-Wan, Padme, and Anakin. The sooner we can get the story to focus on the relationship of these three, the more pay-off you'll have down the line.

- Darth Maul is a murdering bad ass and he is hell bent on killing the Queen. He kills one of her hand maidens very early in the film when. Also screw the "rule of two", he has several cyborg type "hunters" that operate with him. This way our heroes are the underdog from frame 1 creating something called drama.

- Naboo is under full siege and full invasion by the FEDERATION ARMY. All contact to the planet has been cut off. The first half of the film plays a bit like the Die Hard movies. Obi-Wan is a hot shot young new Jedi who was expecting an easy first major assignment, but everything goes to hell when the planet is taken under siege and he has to go underground and find a way into the Castle City of Naboo and he's badly outgunned by the bad guys. He does manage to get the Queen out, but barely.

- In keeping with the original story, they do manage to escape from Naboo but barely with Darth Maul hot on their tails. They crash land on Tatooine, and here Obi-Wan and Padme first meet Anakin. Obi-Wan is shocked by Anakin's inate ability to use the Force. 

- Obi-Wan notices something is wrong with the Federation troops, and voices his concerns to Palptaine and other politicians on Coruscant but no one listens. Queen Padme insist that he become her personal guard, the Jedi want him to watch over Anakin. The Senate declares a state of emergency.

- Anakin being a typical 14-year old in other ways, has a natural crush on the beautiful Queen, but she has feelings for the older, dashing Obi-Wan. Though she being a prim and proper monarch tries to keep these bubbling feelings down inside of her. Obi-Wan doesn't particularly care for royalty.

- The heroes go back to take on the Federation and retake Naboo, but the Republic Fleet is AMBUSHED by Federation Clones (Mandalorians!). What they thought would be a cake walk turns into a disaster as the Federation has far more troops and ships than they thought. The Republic (good guys) engage in a epic space battle, while the Queen and Obi-Wan head down to the surface, the ship Anakin is on is crippled, the pilot has been killed. Anakin is forced to take over the controls and reach out and lets the Force guide him.

- Not only does Anakin guide the ship and its crew out of danger, but he's able to deal a death blow to the Federation's main ship in the process. On the planet surface, Obi-Wan comes face to face with Darth Maul and they engage in a deadly one on one battle that leaves Darth Maul dead (?).

- The Republic (good guys) win but the losses are catastrophic. The film ends with a Senate scene where Palpatine seizes on the fears of the public to be granted the role of Chancellor and to create a Clone Army for the Republic to defend themselves against the Federation's own Clones. The good guys celebrate, but it's clear that a big war is brewing.

So at the end of Episode I, the Clone Wars are just at their beginning, which means Episode II can totally focus on the Clone Wars (rather than wasting another movie getting to that).