I have done this before in my head.
My thoughts were to have the Mandalorians attacking Naboo, previously a backwater planet until it was discovered to have the greatest amount of a rare substance needed for Cloning. The Jedi send people to retake Naboo and rescue the Queen after a group escapes and goes to Coruscant to ask for aid. The Mandalorians sudden attack on the Republic causes a panic and a group of senators start pushing for a draft. The Republic also starts putting more pressure on the Jedi to allow cloning of their Knights, something the Jedi Council has always forbidden.
The Jedi soon realize that the Mandalorians aren't going to be taken down easily and that they are being lead by a Sith Lord (Darth Maul). The Jedi, whose numbers are already dwindling, take a lot of casualties in retaking Naboo. This leads to the Jedi Council to finally approve the cloning of Jedi Knights and Masters.
Padme could be the Queen's younger sister, and Anakin can be a young pilot in their air squadron. Perhaps the Queen dies during the finale and Padme takes her place. Qui Gon could be the Jedi who leads the force to retake the Naboo cloning facility and dies to Maul. Obi-Wan could agree to take Anakin on after he believes that he can no longer be with Padme because she is now the Queen.
The second movie could be the first Clone War, where the Republic finally defeats the Mandolarians. Just as peace seems to be within reach, however, the Jedi Clones start going mad and killing people, claiming that they are the real Jedi and the others are clones. One other thing, all of the clones look very similar to their original source, and each has a name that's derived from the original's name. Obi-Wan's is called "Ben."
By this point, Anakin is a full-blown Jedi Knight, and the development between Obi-Wan and Anakin is mostly showing their friendship. Padme has never married and by the end of the movie Anakin and Padme marry despite the fact that she is queen, as Anakin's now a war-hero. Palpatine becomes head of the Republic, but seems a figure-head.
The final film I never thought about much, so it'll probably be a bit rambling.
RotS has the Second Clone War. The 'madness' has spread from the Jedi Clones to almost all of them, and the Jedi Clones are now using advanced Sith Magic. Naboo and the rest of the Republic are at odds, as they want all cloning stopped permanently. As it is their major export/source of income, Naboo fights this. During an attack on the Jedi Temple, Anakin's clone is killed, and the Jedi use this to try and infiltrate the Clone Army and find out where the Sith are hiding. Obi-Wan is hurt by 'Ben' but survives.
During the time Anakin is undercover, he becomes slowly corrupted towards the Dark Side. The Sith know he's not a clone, because they can manipulate/control those to a degree thanks to Sith Sorcery and them tampering with the cloning vats in Episode I. Maul sends the Clones to Naboo to wrest control of the Cloning Facility and heads to Mustafar to meet up with his Master. Anakin reports all of this to the Council and Republic Members. Before a course of action can be finalized, Anakin goes to stop Maul, as they are talking about fire-bombing the entire planet. Yoda, Obi-Wan, and some of the other Jedi leave to try and rescue as many Naboo as possible. By now, the Queen discovers she's pregnant and is among those who escape. 'Ben' is killed during this time.
Feeling the destruction of Naboo through the force, Anakin falls to the Dark Side and kills Maul. Palpatine reveals himself to Anakin and claims he was against the destruction of Naboo, but he was shouted down. Feeling betrayed by the Jedi and the Republic, Anakin pledges himself to his new master and they make a plan: Anakin and the rest of the clones will meet the Jedi who are coming to 'rescue' Anakin, while Palpatine declares himself Emperor, and orders the execution of the Jedi, blaming the use of the Force as the source of the Clone Madness.
Obi-Wan never reveals the truth about Padme, because he discovers his friend has become twisted prior to getting a chance. They fight, with Vader getting burned. Obi-Wan cannot bring himself to finish Anakin off, however, and leaves. Yoda, Obi-wan, and a few others are returning from Mustafar, when they discover what's happened on Coruscant, and go into hiding. Padme remains on Alderan with another Jedi Knight, but Obi-Wan leaves for Tatooine, where he grew up. He tells his brother, Lars, that he's going to take the name of his clone and live as a hermit, watching them from afar. When Lars asks if he's expected to raise the kid and then just give him up when he's old enough, Old Ben says that the Force will decide.
Pretty rough, especially the third, but I think it'd be better than what we got.