Neo is a program?
I think he is. Think about it. He kinda works like "Ctrl+Alt+Delete". In Reloaded he worked like this because he was going to be used to "Reload"/restart the Matrix (Just like restarting a cpu using Ctrl+Alt+Delete). Now in Revolution he's (from what I hear) going to have to destroy (in this case close) Smith. 'Makes perfect sence to me. But, we'll never know 'till November, right?