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This was a conundrum for me as well, and I came to the conclusion that the architect knows that because an anomoly is an unavoidable eventuality, he needs a failsafe - hostages - with which to hold the One morally responsible for. The people that Neo gets to choose to rebuild humanity will be used as a control for his successor, something for his successor to care about so that he can be easily led down the path the Matrix needs him to choose. His mistake was in assuming that Neo would actually choose the way the others had, and now that he decided to save his girlfriend instead of all of humanity, the Matrix is up shit creek.
Of course, I also totally believe that the Oracle is just another form of Matrix control to try to make Neo choose what they want him to do. Nobody agrees with me, but I think in the trailer for reloaded when she says "The only thing between him and us is you", she's talking to Smith, not Neo. She's a bad guy.
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