Question: When Obi-Wan is told by Dooku that the republic is controlled by Darth Sidious, he does not immediately believe it. Later in the movie he mentions it to Yoda and Mace Windu and he remarks that it does not feel right. Why were the Jedi not able to connect the dots and figure out a pattern when Palpatine stayed in office longer than he should have? That should have been a red flag. Are the Jedi not clued in at all?
Question: If the clones believe Dooku is their leader, why are they against the droids, who are his allies?