When the agents/archietect say Neo is different then the others, it means he has love. Listen. My theory is, the machines let zion exist, so the humans have a place to stay, and when they kill that place to stay, they will get everyone. If everyone was scattered all around, it would be much harder, and resists could be built up. So, eventually "The One" arises in each matrix, and the key maker, the oracle, etc all make him choose the path to the artictect. (This is what the frechmen with the hot wife was talking about, controling people by making them seem to have a choice, but they dont.) They all chose to destroy zion, and save the human race, in hopes of better luck next time. Neo loved trinity, so he picked the other door.