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In believe the counsel are computer constructs similar to the oracle. The computer expected NEO to choose to destroy the human race. The choice is life as a slave or death. "Give me liberty or Give me death" The choice was predetermined NEO had been programmed from the beginning to make the choice. The computers have no intention of destroying the matrix it was a lie they plan on letting Zion believe it has won the war and thus creating a satisfied group. The new disatisfied ones would create a new zion if Neo had chosen the first option.

12 counsel seats, of 23 possible selected to reconstruct matrix. Either my theory is wrong, some stayed in the matrix, or some died. There is a strange connection between Neo and Agent Smith, I think their relation will be the key part of Revolutions. He'll end up helping I think because they both want the same thing, to be free. Even though the trailer suggests otherwise, they'll realize they can't destroy each other because they're related in some way. Agent Smith I also believe violated protocol in killing Neo, that's why Neo was resurrected, because Neo was programmed to be the one, and Smith's vengence and rage (human emotion) took over and altered the program. Is Smith the only free person/machine??