I’m not sure what all I can add to this thread after 10 pages, but I’ll do my best.
Here is how I would have opened the movie:
The movie opens similarly, but when Anakin is told by Palpatine to kill Dooku, he hesitates. Dooku takes this opportunity and escapes. (I wouldn’t have both his hands cut off. I’d let him keep at least one, so he could violently fight his way to an escape pod / ship with his lightsabre.)
Anakin and Obi-Wan both yell for each other to save Palpatine so they can go after Dooku. There are a few wisecracks or sharp words between them as they carry Palpy to their ship together. They both take off after Dooku. Suddenly, Obi-Wan pauses. He sees, or thinks he sees, his old mentor. But he doesn’t understand, and it lasts only a moment.
Dooku heads for the nearest planet, which in my version happens to be Dagobah. Anakin displays his impressive piloting skills by making it through the rough atmosphere in one piece. On the ground, either Obi-Wan or Anakin comments that while the Force is strong here, they cannot sense Dooku, even after they find his ship. “The life force of this planet is somehow … masking him.” (A single line or two will work. This helps explain why Yoda would later hide there. Also, it explains something that doesn’t necessarily need explaining, but sort of fits: Why Luke doesn’t sense that the little green guy he meets is a Jedi Master.)
Palpy has some lines about how dangerous Dooku is and how he’ll say or do anything to survive. He knows that Dooku knows that Palpy wanted Anakin to kill him. Palpy is afraid Dooku might let slip that, oh, by the way, Palpy’s a Dark Lord of the Sith.
Anakin and Obi-Wan each tell the other to remain with Palpy and the ship while they search for Dooku. After a few angry words, Palpy points out there’s a cave nearby and possibly tracks leading to it from the general direction of Dooku’s escape pod. (The audience knows, or at least suspects, that he may have some stronger sense of his former pupil than the two Jedi. The two Jedi just think, at this point, that he has good eyes.) Before Obi-Wan can tell him to stay and protect Palpy, Anakin rushes forward into the cave.
(This is the cave where Luke later sees a vision of Darth Vader.)
Obi-wan is about to rush after him, when again the vision of his old mentor appears. He pauses. It appears the vision is pointing at or trying to indicate something about Palpy. Palpy cannot see the vision, and mentions to the hesitating obi-wan that he will be quite fine and the Jedi should go help Anakin finish off Dooku. Obi-Wan must make the same determination as Hamlet: Spirit of health, or goblin damned?
For a few moments, Anakin is alone there in the dark with his fears. Suddenly, Dooku attacks furiously. His back is to the wall, he knows now that his life is at stake, and he fights like a cornered animal. Anakin can barely keep up with him.
Obi-Wan joins the battle, but in closed quarters superior numbers aren’t much help. Dooku knocks Obi-Wan back with Force Lightning, then yells to Anakin, “You fool! Don’t you see what he’s doing?”
Again, Anakin hesitates. Dooku again takes this opportunity. He lashes out with Force Lightning, and for a moment it looks like Anakin is lost. He is in tremendous pain, pain he won’t soon forget. Not even twenty years later when he sees another Jedi being hit with Force Lightning. He draws on his anger, his hate, his lust for revenge. He somehow diverts the lightning, striking Dooku. Dooku shrivels from the unexpected onslaught.
Palpy appears behind Anakin and tells him to finish Dooku once and for all. His face full of anger and hate, Anakin kills the now completely defenseless Dooku.
Qui-Gon would be interwoven with the rest of the movie. His return wouldn’t be dealt with at the very end with a few measely sentences.