If I was in charge, "Episode I" would actually be where Episode II starts. Stuff that happened in The Phantom Menace wouldn't be brought up, or if it did it would only be through vague allusions. The character of Anakin would be radically different from how he was portrayed in the "official" prequels. First off, there would be no bullshit "Chosen One" prophesy. None of that "virgin birth" stuff either, as I just thought that was creepy (I still like to think Shmi just didn't want to discuss the father, and Qui-Gon was gullible enough to believe her lie).
After watching the Thor movie last week, I couldn't help but think to myself that the main character was almost exactly how I envisioned Anakin to be before the prequels ruined my image of him. I imagined a brave, strong warrior that relished action and excitement, yet still cared about those around him. He would exude confidence and charisma, easily forming lasting bonds with his friends and colleagues. He would be prone to theatrical displays, yet still manage to deliver genuine words of wisdom and stir the hearts of those who heard them.
There would be one major weakness however; he would have a burning need to see justice prevail. To that end, he would begin to dabble with powers of the Dark side, tempted by its promise of power. Thinking he could control it, he would delve deeper and deeper until it would ultimately consume him. By the time anyone realized the full extent of his fall, it would be too late.
When it comes to the Jedi Order, I would definitely change a few major things about it. First off, they would be cool with love and raising families. As Jolee Bindo pointed out in KOTOR, love doesn't lead to the Dark side. Passion can, but only if you let it. Indeed, was it not love that ultimately redeemed Anakin in the end? Also, the Order wouldn't be snatching babies away for training. I always felt that such actions were tantamount to kidnapping, something you wouldn't expect a supposedly noble organization like the Jedi to practice. At least wait until they're adolescents before you begin training.
Oh yeah, and no midichlorians either.
Warning: the following is kind of long.
As for the story, it would begin with the Clone Wars. Palpatine secretly creates a vast clone army to fight (not protect) the Republic and begins by launching devastating assaults on many key worlds. Faced with such a ferocious onslaught, the Senate grants Palpatine emergency powers to enact such measures as drafting vast numbers of soldiers from the population to bolster defenses and increasingly invasive monitoring of Republic citizens in the interest of "security." The effects of the war begin to take their toll, and soon the Republic is faced with additional crises like an influx of refugees along with hunger and poverty. Appalled with this turn of events, the Jedi Order agrees to assist the Republic in their military endeavors, but it's still an uphill battle. As the war drags on, Palpatine continues to consolidate his position as supreme ruler.
It is against this backdrop that the tale of Anakin Skywalker is told. While campaigning with his master Obi-Wan, he takes pity on a sick and weak refugee woman and nurses her back to health. Pity turns to friendship, and eventually blossoms into genuine love. With the Council's blessing, they are married. War calls Anakin away however, and is forced to leave his pregnant wife back on Coruscant. It is while he's away that he eventually succumbs to the Dark side and becomes Darth Vader. When he returns for a brief home leave, she is horrified at the man he has become. After he leaves again she flees to a faraway planet and gives birth to twins.
It is around the same time that the full extent of Palpatine's plan finally reveals itself. Knowing that the Jedi Order will challenge any attempt at complete power, Palpatine orders his secret police to destroy the Senate building. Claiming that the Jedi were responsible for this act of sabotage (along with phony evidence to bolster his claims), Palpatine declares them to be enemies of the Republic and orders that they be hunted down and annihilated. The Jedi, already severely weakened by the war, find themselves caught in the crossfire. The remaining number scatter to the far corners of the galaxy, where most of them will eventually be hunted down by Vader.
With the Jedi seemingly out of the way, Palpatine declares that the Republic will be reformed into an Empire in the interest of maintaining security. All of his "temporary" powers are now permanent, along with a whole slew of new ones that grant him total control of the Empire. Palpatine secretly orders the production of clones to be stopped, resulting in the cessation of hostilities (Imperial propagandists are quick to label it a victory). One conflict leads to another though, as a small group of appalled Senators and activists secretly form a Rebel Alliance to stop Palpatine's tyranny. In some ways this plays to Palpatine's advantage however, as it provides the necessary pretext for maintaining his iron grip on the galaxy. Warfare simply becomes a way of life in the Empire.
To wrap up Anakin's personal story, Obi-Wan tracks him down to Mustafar in order to confront his former pupil. The resulting fight plays out much like the one in Revenge of the Sith, but much shorter and more of a focus on the emotions at play than the set pieces. Vader is left for dead, but manages to survive due to his new Dark side powers. Donning his iconic suit of armor, he becomes the Emperor's second-in-command and a not-so-subtle reminder for the military commanders to remain loyal. On a final tragic note, Anakin's wife is unable to support her children while in hiding. She makes the heartbreaking decision to give the twins to foster parents on Tatooine and Alderaan. The deed done, she dies shortly thereafter due to hunger brought about by abject poverty. Knowing that he can do no more at this time, Obi-Wan decides to keep an eye on the boy Luke, for he may yet be the galaxy's new hope...
...actually Im kidding, because there is no cannon..promotional material doesnt count 
