Finally I start to understand (Matrix spoilers everywhere!!!)
So, the Architect designed perfect Matrices only for them not to work cos humans are fundamentally flawed. By studying human history he was able to improve them but they still failed because there was no choice involved for the humans - they refused to accept the program. As long as humans knew somewhere along the line there was a chance for salvation they could accept it. This was done by the Oracle introducing the concept of the One. However, this also gives the anamoly the power to destroy the system. Thus to safeguard it, they blackmail the anomaly into allowing Zion to be destroyed and being reassimilated into the source code by threatening to shut down the Matrix which would end the human race.
Thus the 5 previous 'Ones' all chose to go through the other door and save the human race and rebuild Zion with the 23 people - but Neo is in love with Trinity, not just humans and so he elects to save her instead. Which is why it's different.
But why does he have powers outside of the Matrix? I'm still working on that.
From reading the transcript of the Neo and Architect conversation.