If you think that bounty hunter logic is flawed, you should hear the commentary track for the deleted scenes. They actually cut scenes out from the movie that feature Jango Fett in the same shot with Dooku because they didn't want Dooku to be revealed as the bad guy. Hmm.
1. Jango says his client is getting impatient in regards to the assassination of Padme. Nute Gunray tells Dooku that he is growing impatient that Padme is not dead yet, and Dooku gives him his word she will die. Ya, totally not the bad guy.
2. Dooku says to Obi-Wan in a very dark manner "It may be difficult to secure a release". NOT the bad guy.
3. Jango is seen landing on Geonosis, the HQ of Dooku. Not the bad guy.
4. Dooku is in league with Nute Gunray, the villain from Episode One. Totally not the bad guy.
5. Dooku tells the separatists that the Republic will agree to any demands they make and the Jedi will be overwhelmed. Getting a clue yet?
Oh, speaking of commentaries, anyone remember that Lucas said he would delve more on the prophacy regarding Anakin being the chosen one in episode II? In the end, all we get is "If the prophecy is true, your apprentice is the only one who can bring the Force back into balance". That's a lot more insightful. Maybe Episode III? "is he not to destroy the Sith and bring balance to the Force?" Oh, now the prophecy says he has to destroy the Sith in order to bring balance. Talk about a last minute change. If the prophecy dealt with the Sith being destroyed thus bringing balance to the Force, why didn't anyone put the two together when they confirmed that the Sith are back and they have this boy who could possibly be the chosen one?!
And the Attack of the Clones commentary? Lucas says we would find out who deleted Kamino from the Jedi files. Do we? No. It gets so much better in the episode III commentary when Lucas pretty much says "if you connect the dots, it all works out".