Neo is the ONE. But SMITH IS THE REAL HERO.
Smith is the only one working to destroy the Matrix entirely (he wants to destroy the machine world and Zion, both are part of the Matrix). Neo exists mainly for the purpose of machine learning, as his code is used to help the machines reboot The Matrix, and make it slightly more perfect based upon what their special agent (Neo) has learned and collected on his journey.
Morpheus and Neo are operating on their beliefs in prophecy. Smith is operating on his own will it seems.
Also, has anyone ever thought that Morpheus is really anarchist hacker, who recruits other hackers via the internet to join his end-times millenarian cult. These hackers commit acts of terrorism against the system. Their digital terrorism is depicted as real world violence througout the film though. And their goal is to lead a revolution that brings the "system" down (hence the millenarian-ism) and they also have their messiah Christ like figure in Neo.