While "The Emperor" is an interesting suggestion as well, THX has pointed out the various flaws with that scenario. The other two feasible characters to be implicated are Sidious, or Qui-Gon. Sidious would be an accurate name, just lying about his status on the Jedi Council. Dooku's reveal of Sidious as the Sith Master, his identity as his apprentice, and Jango's affiliation with him would allow one to connect the dots and solve the mystery. Or would it? Dooku's question of "how the Republic came up with an army so quickly" is confusing in any edit, and would have to be cut. Plus there are so many names and assumptions involved, this option is almost as confusing as the original Sifo-Dyas himself, which is what we are trying to avoid.

Qui-Gon would be a front for Dooku or Palpatine, plain and simple. As THX pointed out a familar character known to the Jedi enchances the importance of the mystery. Also this allows the use for, "...was killed almost ten years ago." I always thought audiences would confuse Sifo-Dyas with Qui-Gon anyway, with that line and Obi-Wan's reference to him as "my master." If the only issue here is dialogue, Ewan McGregor has soundbites all over the place; Star Wars interviews in particular would be a good place to look for "Qui-Gon Jinn," whose name he mentions at least once in the RotS special features DVD (I don't know about the other 2 prequels). Again though, the issue is closure. It would have to be revealed at some point Dooku ordered the clones in Qui-Gon's name to create mystery and the Jedi would have to discover it. I have a couple of ideas but aren't sure if they'd be doable.