Schnizel has been a sleeper villain. He is the one person in the show who understands the true value of sublety. He always says nice things, acts nice, but if you watch his actions are always ruthless in nature.
He befriended Nina, someone he knew was unhinged. Why? So he can have a monopoly on the world's most powerful weapon. How did he do it? Manipulating her by dropping Euphie's name here and there.
In season one, he commended Suzaku on catching Zero, and then was going to blow the shit out of him. I also seem to remember him helping set up the SAR and intending to use it to trap Zero.
Finally, he pulled off a masterful keikaku doori this episode. He ruined Suzaku and Lelouch's reconcilement, and pumped Suzaku for information on the Geass, when Suzaku should have known to keep his mouth shut. Why? Because telling Schnizel about Geass betrays the Emperor's intentions, if Charles wanted Schnizel to know, he would have told him. Finally, Schnizel used Kanon to play off of Suzaku's guilt and make him ready to use the nuke.
Schnizel has had "snake in the grass" written all over him since we first saw him. Also, his monologue at the end of this episode pretty much confirms that he is out to take control of everything, because he stated that he can finally move now that all the cards are in his hand.