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Okay so since I am like king geek I will brake this all down for you. I can understand how the movie seems to be a bit off, but I think it was great.
Neo becomes one with the Matrix, since he is part of the final solution, the machines take him away. Neo was created by the machines to help bring the Matrix and the real world back into balance.
According to what the machines discovered over many many generations, is that the human mind needs a struggle in order to feel in balance. The whole yung and yang theory.
Neo's girlfriend does die. The oracle was part of Mr. Smith since her Code had become part of the Virus that was Mr. Smith so that is why he knew what the Oracle new. Again Smith was a program that became a Virus. We in the development world refer to this as a memory leak or a roge process.
Hope this clears things up for you a bit.
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