I love Concierge's idea-- but the pay off has to be clear: Qui Gonn's purposes were noble-- he was NOT a Sith or a collaborator with Sidious. So Dukoo/Tyrannus needs to call Qui Gonn a useful fool whose idealism let him be used.

It's a really strong idea in that it fits perfectly with his over-the-top faith in Annakin. Qui-Gonn's maverick attitudes are more in line with what's really at stake than Yoda's. However, acting alone, Qui-Gonn does more directly than any other Jedi to aid Sidious. Though Dukoo organizes the separatists, Qui-Gonn finds Anakin, takes him from his mother, makes him a Jedi, orders the clones, and helps make Palpatine the Chancellor. Compared to Qui Gonn, Dukoo's a piker.

I only wish we could add a scene where Sidious and Dukoo go down to the lab to see Sidious creating Grievous out of the barely alive Darth Maul.