Neo is the sixth "chosen one". It looked like the other 6 on the monitors were the previous versions of him, perhaps trapped there, perhaps recorded. But it's probably the Matrix trying to predict Neo's response... The Matrix needs to predict human behavior to control it. That's why they need the Oracle. That's why they need the "prophecy", and even Zion.
Neo is not a computer problem or a computer problem. He is a human that, somehow, is able to exploit the imperfection of the Matrix. Even a 99% perfect Matrix is 1% fallible. But since the failure can be predicted, it can be controlled with Zion and the "prophecy".
If they can control Zion and "the one", they have nothing to fear. That's why they allow Zion to exist and even re-create it. It could be far more dangerous to just let things go free.
Keep your friends closer, and your enemies even closer. For as long as they allow Zion to exist, there will be no true threat to them. Apparently, all other "ones" choose to save the matrix and mankind, and recreate Zion. Apparently, Neo choose differently, what was not supposed to happen.
It's odd, really, because he should have no choice, his choice should be an illusion, or already be made. So it can still be part of the trap, or not. We'll probably learn on revolutions.