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Main villain? Tobi was a shadow, he never the main villain.
Telling someone what occurred isn't manipulating them, Sasuke never sided with Tobi nor cared for him
Kybuui was always always amongst the leaf, he failed miserably and even lost control of the kyuubi himself
Without Kabuto it's questionable whether the Juubi would have appeared without Madara
You're joking right. Kabuto is a big chunk of what's going on right now, certainly, but if it weren't for Obito the war would've never even existed. and yeaah, he is the main antagonist.
He indirectly killed the protagonist's parents
Made the protagonist the person he is today
Manipulated everyone in the Akatsuki
and he toyed with Sasuke's emotions.