Neo is STILL human and can still be gotten to. He isn't perfect code. He is still vulnerable. It's still possible for him to be as weak as he is strong. That's what I took from it, obviously some Jesus-comparisons can be drawn. If Neo's doubts were to overtake him he would be as vulnerable as any human in the matrix. Kind of one of the main themes of the first movie.
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Lord, have mercy on my wicked soul
I wouldn't mistreat you baby, for my weight in gold.
-Son House, Death Letter Blues
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