The bigger issue with this whole plot is that as Pan says, it makes no sense.
1: Why do the Separatists want Amidala dead if she is the one opposing a military response to the Separatists, and as such is the closest thing to an ally that they have?
2: Why did Dooku hire Jango for the job of being a template for the clone army and then act completely surprised at such an army’s existence?
3: Why is Mace Windu, who has intimate knowledge of the plot, not immediately suspicious that the template for the Clone Army seems to be in the employ of Separatists, and why does he kill Jango when he wanted him alive?
4: Why does the Republic not know about the army that they ostensibly ordered? Did the cloners not bother to get any confirmation or send any updates?
I suppose that for the first question, perhaps the Separatists want to push the Republic into a war since they believe that they can win with their secret droid army, not knowing that the Republic will soon have an army of its own. But for this to really make sense, we would already have to know about the secret power of the Separatists and their plan before the assassination attempt, otherwise it seems to be an attack by a Republic hardliner.
For the second question, it seems absurd that Jango would have never discussed with Dooku that the job Dooku hired him for was to build a secret army for the Republic. Are we meant to infer that Dooku knows about and expects the arrival of the clones and is just playacting the fool for the other Separatists in service to Palpatine’s plot? If that is the case, why does he attempt to convince Obi-wan that there’s an evil Sith in control of the Republic, potentially threatening his entire plan? Dooku is painted first as a peaceful idealist, then the strong leader of the Separatists, then a fanatical destructive nihilist, then an easily duped fool, then a duplicitous schemer in league with his avowed enemy. It’s enough to make a person’s head spin, and for this to work we again would need some idea of what this character actually believes so that we aren’t left feeling lost and confused when he does things entirely contrary to his previous characterization.
The third question is genuinely perplexing. If Jango had died in some accident before being apprehended by the Jedi, or even if he was killed by another Jedi before Mace could get to him, it would make sense. But Mace specifically wants Jango alive and then kills him. Furthermore, Mace doesn’t seem to care that he is in the employ of the Separatists. There would need to be an explanation that Jango was playing both sides in this conflict independently of anyone else for this to begin to evade suspicion, but there’s no evidence of that.
Finally, why is there no communication between the cloners and the Senate? Perhaps the cloners are in contact with Palpatine, who is assuring them that everything is good and to keep this under wraps for now, but again, there would need to be some scene where the Kaminoan leadership is in contact with Palpatine, and there’s no indication that this is happening. It genuinely seems like the cloners have been doing this alone for ten years since they don’t even know that Syfo Dias was killed.
I think a lot of the issues here stem from the plot being too confusing and relying on information which is not immediately obvious to the viewer. So perhaps to simplify things, there should be many sides to the conflict, disentangled from Palpatine. If Dooku were a genuine idealist who acts on his own and uses the Dark Side as a means to enact political change, it would give the Separatists an actual identity. Remove the scene at the end of the film where he meets Palpatine. Next, make Jango Fett an independent actor who uses his infamy to contract with both sides of the conflict. This is where the Jedi’s admonition for Obi-wan to avoid assumptions pays off. Have a communication between Nute Gunray and Jango where he is ordered to kill Amidala and make it look like militarists in the Republic were behind it, and use his own discretion in creating this appearance. Jango decides to lead the Jedi to the cloning facility to achieve this end, then goes to his real master to report on the situation. He does not plan on being tracked, however. For the killing of Jango Fett, it would make sense that he is killed by something other than Mace. Perhaps he is killed by the giant beast in the pit, thwarting the Jedi’s interrogation.
So for the new scene, I propose Nute Gunray communicating with Zam Wessel after the assassination attempt on the landing platform and the introduction of the Jedi.
Nute: “Is she dead yet?”
Zam: “No. They used a decoy, and now the Jedi are involved.”
Nute: “The Republic cannot know of our involvement here. My master is sending a bounty hunter to deal with these Jedi…and to help complete your mission.”
Zam: “Is that a threat?”
Nute: “Think of it as motivation.”
This scene lets us know early on that the Separatists are behind the plot to kill Padme. We already know that Nute is in league with Palpatine, and so we assume that either Dooku or Palpatine provided Nute with Jango Fett. That this scene comes after the insistence of Palpatine for security primes the audience to expect Palpatine to be playing both sides. The inclusion of Jango as a later addition to the assassination plot makes sense of the two assassins angle, and Jango being the go-to man for both Nute and Palpatine gives the audience that conceptual bridge that would otherwise short-circuit the two secret armies plots. The fact that Jango hangs around Dooku is a red herring for those believing Padme’s assertion that Dooku is behind the assassination attempts. With the removal of the scene of Dooku and Palpatine at the end of the film, this implies that only Nute is directly under the control of Palpatine and this makes Palpatine’s plan more tricky since he cannot fully control Dooku, the leader of the Separatists.
