I think it would be an awesome twist if Sidious was kept secret until Episode II. Audiences watch Episode I and assume Dooku is the big bad and Maul his apprentice. Go through Episode II knowing about Dooku and suspecting him to make the Empire. And then at the end, we reveal Dooku is just another pawn in a far greater conspiracy.
I know it doesn’t really matter now: everyone knows Sidious is behind it all now, but if we were designing this edit for someone who’s never seen the PT I think this would be a much better way to go about it.
Conceptually, it makes sense, and would work if PM was a differently-structured movie.
Unfortunately it doesn’t work with the overall 6 movie structure since seeing Palpatine’s subtle machinations are key to the entire overarching plot.
I don’t think it’s as difficult as you’d expect.
Step One: Pixalate the Palpatine Hologram and deep-ify the voice, like a mysterious Bond villain.
Step Two: Rotoscope Dooku into some key scenes. I recall a fanedit inserting Dooku into the Jedi Council scene in TPM, but I can’t find it anywhere on Youtube. I probably saw it here through a Vimeo link. But if we added Dooku to the Jedi Council we’d have an establishing scene.
Step Three: The hardest part would be inserting Dooku into the Palpatine / Maul scene. This would be the one time he actually talks, possibly using deleted scenes dialogue. Maybe cut the scene entirely and redub the Maul Apprentice scene in the ship meditating.
So it’s very simple, but enough for first-time viewers to put together the puzzle. A mysterious Sith is talking to Gunray, but we can’t connect the voice (which has been altered through the hologram) to Palpatine. Then, we see a Jedi Council member working with the Sith Maul. So the big bad must be Dooku!
Palpatine would remain seemingly innocent until the big reveal at the end of Episode II.