Keeping on with the idea of Master Jinn ordering the clones...
The script as it is now:
INTERIOR: GEONOSIS, PRISON CELL - DAY
COUNT DOOKU walks into the cell holding OBI-WAN. OBI-WAN is
suspended in a force field, turning slowly as blue electric
bolts restrain him. COUNT DOOKU circles OBI-WAN as they
talk.
...
COUNT DOOKU: It's a great pity that our paths have never
crossed before, Obi-Wan. Qui-Gon always spoke very highly
of you. I wish he were still alive. I could use his help
right now.
OBI-WAN: Qui-Gon Jinn would never join you.
COUNT DOOKU: Don't be so sure, my young Jedi. You forget
that he was once my apprentice just as you were once his.
He knew all about the corruption in the Senate, but he
would never have gone along with it if he had known the
truth as I have.
OBI-WAN: The truth?
COUNT DOOKU: The truth. What if I told you that the
Republic was now under the control of the Dark Lords of the
Sith?
OBI-WAN: No, that's not possible. The Jedi would be aware
of it.
COUNT DOOKU: The dark side of the Force has clouded their
vision, my friend. Hundreds of Senators are now under the
influence of a Sith Lord called Darth Sidious.
OBI-WAN: I don't believe you.
COUNT DOOKU: The Viceroy of the Trade Federation was once
in league with this Darth Sidious. But he was betrayed ten
years ago by the Dark Lord. He came to me for help. He told
me everything. The Jedi Council would not believe him. I
tried many times to warn them but they wouldn't listen to
me. Once they sensed the Dark Lord's presence, it would
then be too late. You must join me, Obi-Wan, and together
we will destroy the Sith.
OBI-WAN: I will never join you, Dooku.
COUNT DOOKU turns to leave.
COUNT DOOKU: It may be difficult to secure your release.
What will need to be changed is the fact that Qui-gon knows the truth. Or some of the truth or at least what he thinks is the truth.
We also ought to take out the bit about the Viceroy of the Trade Federation. Is that at all relevant? Maybe instead of a line about how, while Obiwan doesn't believe Dooku, Quigon did and this is what prompted Sidious to send his apprentice to kill him on Tatooine and at Theed.
And maybe we could introduce the idea of Qui-Gon foreseeing the rise of the droid armies and needing to order the clones to counter them.
The payoff at the end comes when Sidious and Dooku are talking at the end of the movie and reveals the clones they ordered in Master Jinn's name are better than expected. So Qui-Gon never actually orders the clones, but Dooku lies to Kenobi that qui-Gon did. Which lie Obi-wan heard earlier when talking to Lama Su at Kamino.
