Madara has a blood contract with the kyuubi, hence it is his summon as naruto can summon bunta. Nagato is prone to genjutsu as any normal character and amaterasu has been proven super effective. Things like chou shinra tensei isn't getting pass perfect susano'o, Chibaku tensei rendered useless by PS's destruction incarnate sword swipes which are far superior to a Magmata-Bijuudama-Rasenshuriken combo [
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] not to mention that one of these would finish nagato.
True susanoo's unstabilzed form was able to
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a Bijuu-Dama from the kyuubi [
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] with no damage. Chou shinra Tensei would presumably do no harm to its stabilized form; being one of the greatest defenses. Not to mention the possibility of Tenrai Shinsei being a particulary of his Doujutsu. Nagato stands no chance whatsoever.