I'm not sure that the PT would need to be drastically different form what we got, just made better and eliminating the nonsense. You could still start at a somewhat happy point, where the majority of the galaxy is at peace. The trilogy should gradually build in tension and drama until the climax of the third film, much as it tried to do originally.
For simplicity's sake, I concur that Episode I could be something like this: http://www.youtube.com/watch?v=VgICnbC2-_Y.This guy has some great suggestions on how a few tweaks to the current version could be vastly improved. I would add that nothing should take place on Tatooine in the PT (why would you hide the bad guy's son on his home planet? Shouldn't you try to be a little deceptive?!). We would also need to throw in an apprentice of Obi-Wan's (let's call him Starkiller) who has already been in training when Anakin comes along and who is a little jealous of the new kid.
Ep II picks up about where AotC did - Anakin is growing in skill and has been on many successful missions. He's a completely different character than what we were given, because he has to be noble, likeable, and charming. But he is always curious about how much more he can do, and Obi-Wan has to do most of the training himself because Yoda (whom we never see) and the Jedi Council are still fearful about giving Anakin too much freedom. During this film, we see Starkiller get pulled away from the Jedi by a dark-robed figure to join the other side, just in the way the Emperor tried to lure Luke to the dark side. Obi-Wan realizes this through the Force and admits to the other Jedi that his apprentice has turned to the dark side. Keep the plot about Anakin falling in love, but make it believable. She should still be from a planet other than Alderaan, though, for the same logic used above for Tatooine.
Ep III plays out similarly as before, except that Anakin is a likeable hero throughout. The Jedi are figuring out who the dark-robed mastermind is and tracking him down. Meanwhile, a hooded figure (we know it to be Starkiller) has been wiping out Jedi. Anakin wants the glory for being the one who tracks down Starkiller and puts and end to the conflict, so the Emperor plants information that leads Anakin to a trap. He, Obi-Wan, and a team of Jedi go to investigate and are separated. Anakin is alone in a dark room with Starkiller and the Emperor, similar to the throne room in RotJ. He and Starkiller begin fighting and he realizes he can't win. The Emperor encourages him to give in to his anger and hate, because it's the only way he can overpower Starkiller. Anakin begins fighting back much more aggressively, and he and Starkiller are evenly matched. The climactic moment: we see their two silhouettes fighting; the Emperor Force-pushes them, disarming both. He blasts one of them with lighting and yells "Finish him!" The standing silhouette Force-pulls the red lightsaber to himself, ignites it, and slays his opponent. Obi-Wan and the other Jedi feel the impact from the next room through the Force, and one turns to Obi-Wan and says, "Your apprentice is dead." The surviving fighter, smoking from getting hit by some of the lightning used on his opponent, is weak and breathing heavily. He and the Emperor escape. The Jedi, knowing the mission has failed and the enemy has escaped, retreat.
In the remaining scenes of Ep III, we see a robed, masked version of Darth Vader in charge of hunting down Jedi. Remaining Jedi are told to hide out on remote systems until they can find a safe place to regroup (which never happens as Yoda and Obi-Wan end up being the only ones left). Padme gives birth to twins. We know one is a boy, we don't know the other's gender and neither are named. She encourages Obi-Wan to help keep the children separated for their safety as she is invited by Bail Organa to live on Alderaan. We see Obi-Wan taking the boy to Owen and Beru on Tatooine. Roll credits.