This one is even more sketchy, but this is what I have.
* Anakin has been training to be a Jedi Knight.
* Qui Gon is still an apprentice and is chaffing under Obi Wan's tutilage now.
* The nature of the Jedi is different from the actual prequels. In those films, the jedi were rather institutionalized with a rigid structure and such. My Jedi are much looser. ObiWan calls them together to try to get their aide against the Cloans, but they are reluctant as it is their duty to defend peace, not to be involved in political struggles. If the Cloan armadas conquer, they will continue to make peace under their regime.
* Obi Wan's most vocal opponent is Mace Windu who is displeased with Obi Wan's exploits as they are a bit garish for a Jedi.
* A mysterious figure in black has been killing Jedi Knights. This person wears a mask to conceal his identity
* Obi Wan and his apprentices go to find this person on a planet with poor atmosphere, so they wear breathing equipment which obscures their faces and alters their voices. the two apprentices search together and then one kills the other. ObiWan find the pile of clothes and Anakin's lightsabre, which he takes.
* Obi Wan confront the figure in black and learns that the person calls himself Darth Vader and is one of his apprentices. They battle and vader is plunged into the lava.
* ObiWan returns to the front of the Cloan battle and finds out that the Jedi have sided with the Cloans. In the Chancellor's Palace, ObiWan and Mace Windu battle, but it turns out that the reason why the Cloans were attacking is because the chancellor of the Republic is evil and Obi Wan's loyalties had been sadly misplaced.
* Vader returns as a mechanical monstrosity and a battle ensues, jedi die but obi Wan escapes.
I kind of like the reversal here with the Cloans being actually the good guys all of a sudden because the chancellor is, you know, the emperor and stuff. It makes the story about the failings of Obi Wan, how is somewhat non-jedi ways led to the downfall of everything he holds dear.
Obviously, Bail and Amidala need to be in here somewhere, but it's sketchy as of yet. I think Anakin and Amidala's marriage needs to be stated at some point. They kind of have to be married since I doubt that children out of wedlock would go over well.
My main purpose here is to keep Vader's true identity a secret until ESB. Imagine the shock for someone who first sees these movies in order. This actually strengthens the whole 6-part series, tying them together. The actual prequel weaken this. Sure, we get to see Anakin's fall from grace, but it makes the reveal in ESB weaker because we already know this.
Part 3: The Fading Light
Still sketchy, but this is what I have:
* The chancellor declares the Republic is now an empire. "And democracy dies to thunderous applause" appears in the opening crawl, rather than being shown. Also the Jedi are declared outlaws. This is all in the crawl.
* Obi Wan has left behind the name of Obi Wan as it is no longer safe, so he goes by Ben. Note the tie in to the first episode! Woo!
* Amidala has secretly given birth to a son, which Obi Wan thinks should be hidden.
* the Emperor and Vader learn of the child and begin hunting for the son of Skywalker
*Obi Wan takes Luke to Dagobah and consults with his master, Yoda. Yoda tells him it is not safe to leave the boy here as the emperor is hunting down the Jedi and both he and Vader will not rest until they find the son of Skywalker.
* Vader confronts Amidala about her son and kills her when she refuses to tell him where he is.
* In a final battle, Vader and Obi Wan clash over the child, with lots of hiding and stuff, like the sabre battle in ESB. Which ends with vader seizing the infant and then obi Wan slices off his hand (mechanical) and tries to catch the child but the blanket unravels and the baby falls into the lava (Lava? Again??)
*years later, Obi Wan goes to tatooine where Owen and Beru have set up a moiture farm and tells them it is now safe as the emperor thinks Luke is dead and he has come to take Luke to train him to be a jedi Knight.
*Owen refuses to let Obi Wan take Luke and says that Anakin should have stayed with him and not gotten involved. ObiWan warn Owen to not get in the way of another's destiny and departs.
* Luke comes out and asks who that man was. Owen says it was no one important. They all look at the starry sky. A shooting star goes by. Beru points to it and says "Look! There's you're father. Owen gives her a sharp look and tells Luke that maybe someday he'll tell Luke all about him.
Fade out.
I don't think much here needs explanation. Making Luke a central item to drive the plot makes this a strong story. Making it appear that Luke is killed helps explain why the Emperor is not still searching for him. Bringing Luke to Dagobah adds to the lines Luke says in ESB about how Dagobah is familiar like he'd been there in a dream. I might even have a scene with Leia which Bail says is his daughter and he and Amidala exchange a look which becomes apparent in RotJ. I do like the ending and how the trilogy is bookended by a shooting star.
In any case, this is my idea for a prequel trilogy... at least at this time. I now welcome comments and rocks chucked at my head.