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Gendo may not have personally put too much faith in to Shinji, but at least Seele foresaw it. I don't think Gendo is as naive as the way he led Shinji to believe. Also, it strikes me as too convenient that his backup plain in Rei basically was the key to the salvation of mankind. Gendo must have foreseen what was going to happen to a degree even with his infatuation with Yui.
It still doesn't make me like Gendo any more as a person, but I still can't find any other single character who made it more possible than Gendo. Shinji was basically just along for the ride. Ever since episode 1.
And as for the whole 'right choice' thing, I don't think there was much of a choice to begin with. Either ends up with humanity progressing in some forms, sacrificing their current forms in a major, cataclysmic way. Though I do think the illusion of choice was there.
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