Obito is the main villain by far. He's been in the show more, and he's responsible for more acts and manipulating more people.
He caused the Kyuubi attack, killed Kushina in it and indirectly caused the death of Minato.
Helped Itachi kill the Uchiha clan.
Controlled the Mizukage and, if anything, sat by and let the Bloody Mist flourish.
Plotted the death of his partner, Deidara. Or outright hoped for it. . Would be better.
Expected the death of Itachi, and saught to use Sasuke as a pawn.
Is responsible for the whole war.
Manipulated Nagato into perverting the Akatsuki.
Madara can only really say that he corrupted Obito. And 'manipulated' Obito. But. . I don't see it as Manipulation (Just yet aleast, I'm sure we'll see more of their past soon) as Obito desperatly wants to finish the Infinate Tysukuyomi too.