DuracellEnergizer said:

If only Dooku has been genuinely opposed to Sidious instead of being his undercover Smithers. He would have made for a far better, far more complex, character.

Totally agree. Would have loved to have seen Dooku not even know he was a Sith; like an undercover cop gone dark.

Maybe have it so the Jedi sent him out to sniff out potential Sith but they lose contact with him, and then just abandon him out there, claiming he "left" but basically just giving him up for dead, which would account for Dooku's dislike of the Jedi and his want to destroy Sidious.