shanerjedi said:

Didn't he mention to Obi-Wan in AOTC how the JC wouldn't believe him?

Nope, unfortunately. Otherwise it'd be a hell of a lot easier making it more plausible.

shanerjedi said:

You could certainly have Dooku in TPM at some point. Maybe at Qui-Gon's funeral? Maybe in the JC scenes?

Those are doable because there's little camera movement in the JC scenes.

Whether it's doable or not, simply having Dooku at the funeral isn't sufficient in conveying anything new to the audience. For a new viewer it wouldn't make anything any clearer than before unless new dialogue can be constructed (but there's no accompanying lipsync) - Dooku still leaves the order and we don't know why and it's still not suggested he went to the Jedi with his suspicions. Unless you refilm Christopher Lee having an argument with the rest of Jedi about the corruption he senses in the senate, then nothing changes.

This is why I'm hoping the Jocasta Nu scene will be included in the Blu Ray release as a deleted scene. In this scene she tells Obi Wan what a great Jedi he was, and that he was one of only 20 Jedi to have ever left the order, and that he did so because he was discontent with how things were being run.

That scene at least hints that he's had a disagreement and voiced his opinion on the matter.