I really wanted Lucas to focus on why the Jedi Order is so important in how it keeps Jedi from taking the "easy way out" and not turning to the dark side. Bring up the old Sith hierarchy, and how it took the Order being created to truly "destroy" the Sith. However, in the weeds you have Palpatine. Strong in the Force, and dedicated to the old religion of the Sith. He has his apprentice Maul, who is his go between to the Mandalorians, who want control of the outer rim territories. Palpatine sees his way to truly gain more control by manipulating both sides.
So since the Jedi Order has kept peace for a "thousand generations" it was going to take a true conflict to destroy the Jedi. You could have Palpatine, Senator at the time, slowly manipulating the Mandalorians into using their clone facilities to create an army that would truly be a conflict for the Jedi to fight. Episode 1 would be in the middle of the war. The Jedi are being wiped out, and stretched too thin. In doing this, Palpatine is given his "emergency" powers by the Senate to form his Storm Trooper army, since the Jedi are not able to defend the republic. Maul is also the enforcer for the Mandalorians, and a strong Force on the dark side. Since the Jedi haven't encountered the dark side in so long, no Jedi can defeat him. Enter Anakin, a young pilot making waves in the Outer Rim with a ragtag fleet fighting the Mandalorians. Obi-Wan is sent out there to help, and senses how strong in the Force Anakin is. He brings him before the Order, the Order agrees that Anakin should be trained in the Jedi Arts, even though there are some concerns about his age, and how reckless he is. Anakin requests that his young wife also be brought under the Orders protection. The Jedi agree, despite reservations about his age, and his recklessness.
So, that sets up the next movie. You can have Maul basically waging war on the Jedi himself, and the Order is barely hanging on. Palpatine, who has the power of foresight, senses how on the brink Anakin is, and how strong in the force he is. Since the Emperor is all about control, and keeping those who are strong enough in the Force to defeat him under his wing, sets up Maul to kill Padme. During the assassination attempt, Padme is barely saved by Obi-Wan, and is taken into hiding by the Jedi Order. Anakin, now full of hate, is warned by Obi-Wan and Yoda to not use the dark side to defeat Maul, and to let Obi-Wan handle it, since he far better trained. Anakin does not listen, and defeats Maul by using all of his rage. The Emperor then presents his true self to Anakin, and informs Anakin that the Jedi Order will not let him and Padme live, because of Anakin utilizing both aspects of the Force. Anakin, now being seduced by the dark side and is blinded by it, confronts Obi-Wan, and their duel takes place. Obi-Wan wins, Anakin is badly injured, and is saved by Palpatine, who puts him in the suit to keep him alive.
Episode III would then be all out war. Vader hunting down every last Jedi until he gets Padme back, Obi-Wan being the last line of defense for Padme. The Emperor, now in full control, ends the conflict with the formation of the Empire, and the Mandalorians, who have their cloning facilities destroyed, have no choice but to surrender. Palpatine declares the Jedi Order no more, since the Empire will now protect the galaxy.
The last third of the movie would be Anakin confronting Obi-Wan. They have one final battle, and Padme tries to stop Anakin from killing Obi-Wan, who in turn with his rage, mortally wounds Padme. Since he is so blinded by his anger towards the Jedi Order, he then realizes that Padme is pregnant. He does not sense any life in Padme, so he leaves her behind with Obi-Wan, telling him he's "failed her".
Obi-Wan rushes Padme to his ship, and is able to bring her back to life. She is badly injured, but the babies are safe. Obi-Wan and Yoda, the last remaining Jedi, decide to separate the twins to keep them out of the reach of the Emperor and Anakin. Obi-Wan reaches out to an old family friend the Lars on Tattooine, and Leia is sent to Aldeerran, under the protection of the Organa family. Palpatine, now with his new apprentice, declares Anakin is no more, and will henceforth be known, as Darth Vader, the Emperors justice for the Empire.
The last shot is Beru and Owen holding baby Luke in front of the two suns.
I've even gone as far as to write some fanfiction on this. I'm sure its shit, but this is always how I envisioned the prequels being set up once they were announced.