I’ve always liked the idea of Dooku being just a rogue Jedi, because it makes Dooku a more complex character. I think a big issue with that though is that it would contradict Dooku’s portrayal in the Clone Wars, for those who enjoy the show.
I kinda wish there was a way to have Dooku aligned with Sidious, but imply that maybe Dooku has joined the Sith with the intention of trying to destroy it from within. Like, maybe that was his motivation for joining Sidious initially and he thought he would be strong enough to resist the temptations of the dark side, but as the war goes on, we see Dooku becoming more and more cruel.
Some of the new canon material, like the recent Master and Apprentice novel, implies that Dooku believed he might be the Chosen One, so this would kind go along with that idea. In this way, Dooku’s conversation with Obi-Wan about wanting to destroy the Sith would actually be true.
Maybe if you were to cut/alter the portion of their conversation about the Trade Federation being betrayed by “the dark lord” and coming to Dooku for help, and maybe replace it with something that one could piece together about him finding the dark lord and joining him.
Maybe when he almost kills Obi-Wan, you could have Dooku say “I’m sorry, Obi-Wan”.
And then in Revenge of the Sith, right before Anakin kills him, maybe Dooku could start trying to say something, like wait/stop/no/he is-, some variation of that.
I kind of like the idea of Dooku joining the dark side in the belief that it was a necessary evil, but being corrupted along the way. And it wouldn’t blatantly contradict the Clone Wars, because you could still keep his red lightsaber and him working with Sidious.
This above is more or less how I intend to represent Dooku in my edit (though he won’t be a Sith). He’s aware of Palpatine, and his machinations, obviously certain things will have to be inferred due to the material available. I thought by adding Dooku to the Senate scene in TPM it draws a link between him and Palpatine, and the fact that he turns and walks away will show his disillusionment with the Senate.
He would be wielding a blue sabre in my edit.
On another note, I always felt Obi-Wan should be wielding Qui-Gon’s green blade at the start of Attack of the Clones.