Trivia: It's been said that Neo being an anagram for "one". I think it's more important to realise that Neo means "new". His real name is Thomas Anderson. He is called Thomas at the beginning of the movie, when he doubts the truth -- that the world as he knows it is not real. Thomas is the "doubting" disciple in the Bible. Moreover, Anderson means "son of man". Hence, Neo Anderson is the New Son of Man. The biblical references go on and on... Trinity, Nebucadnezzar (the name of the ship -- in fact, the name plate on the ship makes reference to a verse in Mark chapter 3), Zion... So not only is Neo "the One", he has gone from being the doubter to the new son of man.
Agent Smith: I'd like to share a revelation that I've had during my time here. It came to me when I tried to classify your species, and I realised that you're not actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment; but you humans do not. You move to an area and you multiply, and multiply, until every natural resource is consumed and the only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus. Human beings are a disease, a cancer on this planet, you are a plague, and we...are the cure.
Question: What if they were to destroy the Matrix, then all the humans would be free but the problem is where would billions of human beings go? Zion, the last city, can't hold them all and they can't live in the tunnels or above the earth's crust because there is no food or water there. The whole war doesn't seem to be well thought out and seems like a big plot hole on the Wachowskis part.