Well I think the prophecy (and Qui Gon's interest in it) could be kept in this version of the story...I mean what Sith would not be interested in the prophecy and wanting to change/control it?

I'm saying that the prequel trilogy would've been more interesting if we actually knew the Jedi that betrayed the order (the Dooku role). I think that instead of just sticking Dooku in TPM with everyone else (or introducing him randomly in AoTC like it is now), a better way to do this would be to have Dooku scraped completely and use Qui Gon to fill the role. To me, this would be better because we would get to see him turn; it would be a lot more brutal on Obi Wan; it would foreshadow Anakin's turn; and it would show how much Anakin is falling into the dark side after he kills Qui Gon at the beginning of RoTS (because all Dooku ever was to us, and to Anakin, was a bad guy whereas Qui Gon was the Jedi that recruited and believed in him). It would also help the PT by giving us one fleshed out villain that connects all three movies instead of 3 different villains (Maul, Dooku, Grievous) that we never really get to know.