AOTC had a lot of future event mirroring (Jedi's face beasts in a gladiator setting, Padme wields a chain, Anakin gets arm lopped off, etc.). I think Count Dooku's revelation about Darth Sidious was one of them. It sounded to me that he was offering a genuine partnership with Obiwan to overthrow Sidious, much in the same way Darth Vader treated with Luke Skywalker in "Empire Strikes Back." I never figured out whether Darth Vader was being serious, and don't know whether Dooku was too, but I rather enjoyed the ambiguity.
Everyone is right about the Sidious' motivations for having two armies. To me, it also sounded as if the thinning of the Jedi Council was an intended side-effect. Windu threatens Dooku for the loss of Jedi life, and we all know that eventually the council will be winnowed down to two members. Of course, in all the books the Jedi council dies in a single spaceship explosion, but Lucas is not beholden to that.
Which reminds me, Dooku must be the Dark Jedi that dies on Dagobah. That's a battle I wish to see!
James
P.S. I also liked the idea that Palpatine was a clone of Sidious, but I think it's rather clear from Ian McDiarmid's makeup that the Senator is looking more and more like the watery, pale dictator of the later movies. His speech is becoming more reedy and sly, too.
P.P.S. I thought it was Sidious that ordered the clone army. Would make sense that he would be able to keep the clone army hidden seeing as he's been able to keep himself from the Jedi council's collective eye.