Is'nt that obvious? Tobi kept secrets from Itachi, he said it in the manga himself. Itachi was fooled:That guy talks about Itachi wanting Tobi/Shisui to be his mentor yet Itachi always thought Tobi was Madara. If he knew tobi was Shisui why would he put amaterasu in Sasuke's eye to attack Tobi? I get it's just a theory for fun but it has a lot of holes.
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Its already been hinted, Itachi's witness accounts are'nt credible. What , lol do you believe him nd think Tobi's really Madara? Madara's an edo tensei, of course Itachi was deceived.
Itachi did NOT know the real identity of Tobi.