How to fix the Star Wars prequels - an open letter to Disney, should they ever decide to remake them.
Episode One: We begin with teen Anakin in the service of his mentor, Obi-wan. The few parts of the Phantom Menace that we need to know (that Anakin was a slave, that Palpatine rose to power without deserving it, and that Anakin and Padme crossed paths at some point in the past) are explained in expository dialogue. We see Anakin learning the ways of the Force similar to how Luke trained with Yoda. Anakin is extremely strong in the Force, but he's a bit arrogant (not whiny) and it's hard to get him to focus on the need for peace and justice rather than just more power. Through this mentoring and through a few incidents where each has to save the other's ass from time to time, they learn to trust each other and become good friends as well. By the end of the film, the rise of the Sith is apparent when Darth Maul appears and has an epic light saber 3-way with Anakin and Obi-wan. Maul escapes (barely) and our heroes begin preparing to take on the rise of the dark side in the upcoming Clone War.
Episode Two: It's discovered that one of the Republic's former leaders, presumed dead, has actually gone into hiding and has ordered the creation of a Clone Army. Palpatine convinces the Senate that he was in on it and had actually sent the leader into hiding to spy on the Federation, which are supposedly controlled by the Sith. The army was being grown just in case it was needed and it totally is, so this is a good thing. The Republic declares war on the Federation, with only a few leaders opposing. One of those leaders is Padme - and the Jedi are assigned to protect her, leading to Padme and Anakin crossing paths again. He becomes her bodyguard. Anakin and Padme fall in love and have actual romantic conversations, none of which involve Anakin's distaste for sand. Obi-wan and the other Jedi are absent, off trying to help the Clone Army locate and root out the Sith in the Federation. The formerly missing Republic leader (who is called pretty much anything that isn't "Dooku") is discovered in a secret meeting with some unsavory characters. He tries to convince Obi-wan that the Jedi are on the wrong side of the war, that Palpatine knew nothing of the Clone Army, and that it's Palpatine, not him, who has gone to the dark side. Obi-wan doesn't believe him and kicks his ass.
Episode Three: Anakin is appointed by Palpatine to be the Jedi liaison between his office and the rest of the Jedi Council, since they're all out at war. Palpatine learns of Anakin's love for Padme and begins to use that to get on his good side. Palpatine explains that love is something that should never be denied, and that the Jedi code that forbids him marry her is so much bullshit. He goes on to explain that the Jedi code is put in place so that Jedi will remain controllable and subservient to the Council. If not for the limitations of the Code, the Jedi would have no need to obey the Council's wishes - they would be far too powerful. Love, he says, is one of the keys to obtaining that level of power and the Jedi Council would forbid him to marry Padme because they're afraid of him becoming too much for them to control.
Obi-wan is informed of Anakin's romance with Padme and forbids he see her again because his feelings and emotions will interfere with his training and it's against the Jedi Code. Anakin loses his shit over that and the two nearly come to blows over it. Both stop just short of drawing their light sabers, but their friendship is destroyed.
Obi-wan reports to the Jedi Council, who remove Anakin from any further training, citing his rebellious nature. Anakin talks to Palpatine, who promises to teach him how to focus his love for Padme into a stronger presence in the Force, which will give him more power than any Jedi. When Anakin hesitates at the idea of being "against" the Jedi, the very group of people he's aspired to join, Palpatine convinces him that he's been duped this whole time. The Jedi Council, he says, are merely a cult who don't allow their knights to love because they can't control anyone with that much power. "You will never be as powerful as you can be if you aren't allowed to love." Palpatine begins secretly training Anakin.
The Jedi are all out on the battlefront when Palpatine executes Order 66, a command encoded into the Clones' training that turn them against their Jedi leaders. Most Jedi are killed and the few who are left return to Coruscant only to find that it was Palpatine who gave the order. Worse, Anakin is training with him and has become very powerful.
Palpatine sends Anakin to Mustafar and then meets up with Padme, who had given birth to twins a few days before. He kills her after being unable to get her to disclose the location of her twins.
Meanwhile, Obi-wan sets out to find Anakin to turn him back to the light before it's too late. They have their epic duel on Mustafar and Anakin is badly burned and nearly dead.
Palpatine arrives in time to save him and fashions a mechanical mask and suit that will provide life support. When Anakin becomes conscious again, he asks where Obi-wan is. Palpatine tells him that Obi-wan not only left him for dead, but had gone back to Naboo and killed Padme and the twins so that Anakin would no longer be tempted by her. Anakin vows to become as powerful as he can in order to bring down the "cult" of the Jedi and get revenge for the murder of his family.
There. No Jar-jar, no midi-chlorians, no trade disputes, no "Yipee!", and no "she died of a broken heart" bullshit. I'm sure that there are some tweaks that need to be made to it, as I just sorta threw it all together as I typed. It's STILL better than the prequels we got, though.
Fixed it for ya.