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Well apparently the series assumes that the human mind and the Machines' computer systems are cross-compatible. The Matrix can upload information to someone's brain (all the people who are plugged in), so who is to say a brain, when connected to the Matrix (as Bane was when he got 'infected'), can't be altered so severely that someone's personality stays changed, even when he or she is unplugged ? I think this is what happened.
Neo can't do the cool Kung Fu because everything he does in the Matrix is based on mental capacity, not physical capacity. In the Matrix, you are bound by the rules of the Matrix and your own mind. In the real world, you are bound by physics and the limitations of your own body.
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You don't know what you don't know.
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