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Bane was turned into Smith because he got infected inside the Matrix. His mind changed while inside the Matrix. Just like if you die inside the Matrix you die in the real world, his mind was changed in the real world.
Neo had a connection in the real world to the machines. This connection allowed him to blow up the machines, but since it was only a connection to the machines it didn't give him his kung foo abilities nor could he fly or anything else like that. He was in the real world and therefore had to abide by the rules of the real world with no way around it. He just had the connection to the machines and nothing else.
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When life gives you lemons, sqeeze the juice into a squirt gun and shoot people in the eyes
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