I love that Neo figured out the only way to win was to give up.

He "became" Smith, just like Jesus became sin, allowing the machines to destroy Smith, just like God destroyed sin through Christ.

I understand that the machines could not just unhook all humans from the Matrix - they have to give each of them a choice; choice is the greatest good that neo aspired to.

I am somewhat perplexed by the comments of the little girl at the end; she "created" the sunrise for Neo. Did the machines perhaps give humans some measure of control over their environment within the Matrix as an inducement to remain connected?