Personally, I find the occurances of The Phantom Menace to be the product of the Expanded Universe's biggest problem: minimalism. Though we like to credit Karen Traviss and Timothy Zahn with it, Mr. Lucas has interlaced his saga with minimalist proportions for a tragicomedy that is supposed to be set on a galactic scale. Though the events of the plot are cogent enough, I have a hard time believing or accepting the idea that the extraordinarily brief horrors of one backwater planet would be enough to be the focus of an entire movie. Yes, I realize all too well that it was basically a set up to introduce Anakin and elevate Palpatine to the status of Chancellor, but that's it. I can understand this story being the personal tale of Skywalker and, in the big picture, Palpatine's rise to power, but the entire movie shouldn't be a basic set up for just that. For example, in Revenge of the Sith, we had enough action and conflicts of other characters to deal with, numerous battles on numerous planets. That is what Star Wars should be about: the trials and tribulations of multiple characters in multiple theaters all working to drive the plot of the larger characters; it needs more background noise, in essence. The Phantom Menace lacked that, big time. And the pod racing, Jesus Christ, for a superscene that was designed to depict groundbreaking special effects, I was unmoved. I have only watched that scene in its entirety once, I believe. Everything should have a purpose to the narrative.
So, to that end:
a.) My first suggestion would be to have the first movie take place when Skywalker was a teenager or young adult, akin to when we were first introduced to Luke Skywalker. Perhaps we could have flashbacks of his discovery by the Jedi and his enslavement, but nothing to focus the entire exposition of a movie about. Though his background is important, his future is far moreso.
b.) No Naboo. Or if you're absolutely determined to keep it in, don't make it the center focus of the entire first movie. It's farfetched that Palpatine could springboard to ascendance based off of the whining of one misbegotten planet. Design a better springboard for him to leap off of.
c.) No Maul. Honestly, I like the idea of Sidious's silent and unstoppable minion, but he wasn't necessary at all. For all intents and purposes, his position as the assassin of Sidious's potential rivals and enemies was undefined in the movies, so he is not necessary. Bring in Count Dooku much earlier, perhaps in the twilight of his Jedi career, or before he was seduced by the Emperor, or in the process of. For an interesting character who is very essential (a Jedi dynasty of sorts between him, Qui-Gon, Obi-Wan, and Anakin is very deep, in my opinion), he needs more screentime.
d.) General Grievous, as written by Matthew Stover, is a more badass character than anyone this side of Gilad Pellaeon, Turr Phennir, or Moff Tarkin. Use the movies to flesh out his tactical brilliance and his proficiency in dueling.
e.) Keep Qui-Gon Jinn. Liam Neeson is amazing. Perhaps he can die in the first or second movie, but his presence can be still used as the guiding focus between Obi-Wan and Anakin. Since Qui-Gon outranks Obi-Wan, we could keep the rapport between him and Anakin, and Qui-Gon would be a great excuse for Anakin to model himself off of: reckless and all that, instead of spontaneously being an ass like he is in Episode II. Perhaps Dooku could kill him as a test by the Emperor?
f.) NO MINIMALISM. Make it clear that the Republic vs. Separatist movement takes place in a galaxy with millions of worlds with tens of thousands of ships. We might not have the budget to see them all, but make it obvious. Clone Army must constitute billions of soldiers.
g.) Place Jedi in a healthy light. These guys are reputed to be demi-gods. We don't need you to wankify their feats, but cement their reputation as feared warriors by the opposition that only great numbers of the strongest enemies can face.
h.) No droids. Based on early EU, the Clone Wars were intended to be clone on clone warfare, used by both sides. Clones versus machines really don't add that humanizing light to the Separatists. Lucas states in the opening crawl of Episode III that "heroes are on both sides." The Confederacy, as a whole, should be no more or less evil than the Republic. Their soldiers should be flesh and blood as well, to remove the feeling that they are all unambiguously evil. It was a popular movement for a reason.
i.) Tarkin, Pellaeon, Sate Pestage. Those are major EU characters who need movie time. Mas Amedda and Sly Moore? Not so much.
j.) Skywalker is the main character. Get an actor who can actually... um... act.
k.) No half-assed ideas. Such as Palpatine's disfigurement. Even as Episode II commences, we see Palpatine slowly being aged and withered by the dark side. The idea that Windu's electrocution somehow "ruined" his mask is ridiculous, nor is it clear cut for anyone who doesn't bury themselves in EU.
l.) George Lucas can supervise and direct the storytelling and narrative. But in no uncertain terms is he to direct or write the script.
That is all for now.