I always liked the idea of the clone army being this big Sith conspiracy. However, the way it is presented makes the Jedi look like idiots for not ever finding out. I would make a minor change to the end of AOTC. Obi-Wan, Mace and Yoda realize now that Dooku is a Sith and impersonated Sifo-Dyas to the Kaminoans in order to create the army. The scene would play out as follows.

OBI-WAN

Dooku was strong with the dark side. I believe he is this Tyrannus person the bounty hunter spoke of. In that case he must also have been impersonating master Sifo-Dyas. Dooku ordered this new clone army.

YODA

The one to delete the Kamino file he must have been.

MACE

Why would the Sith Lords do this?

YODA

Intricate their plans are. For certain one thing is, they need a war.

OBI-WAN

And the Republic couldn't fight without troops. If what he told me on Geonosis was true, about a Sith Lord hiding in the senate, then this war is a Sith operation with Tyrannus on one side and Sidious on the other. This is a plot aimed at us. At the Jedi; to bleed us dry. To make us into something we were never intended to be.

Mace lowers his head in agreement.

OBI-WAN

I know you’ll both agree the Sith have succeeded in doing at least that.