The character with the strongest case as mankind's savior is none other than Hugo Weaving's brilliantly-realized Agent Smith. While it may seem crazy at first, the evidence is pretty compelling. As pointed out in a video from Film Theory, while Neo is able to do things like fly or fight like a super-soldier, there isn't a whole lot of Matrix manipulation going on with this guy. Smith, on the other hand, goes full virus mode, changing things at will and assimilating inhabitants.
As far as being a man born in the Matrix, Neo was actually born in a pod and shows up around the sixth iteration, according to the Architect, whereas Smith suggests to Morpheus in the first film that he has been around since the beginning. In that interrogation scene with Morpheus, Smith shows very human characteristics, unlike the other programs. He unmistakably rebels (a quality of The One) when he removes his earpiece, disconnecting his communication with the system he is supposed to protect. He then goes on to discuss smell and taste, attributes only a living being would likely know anything about or think to use when making a point.
And then there's the element of the prophecy that involves returning to the Source to reset The Matrix. Neo does accomplish this goal, but the end result only occurs after he is assimilated by Smith. Could that have been the plan all along, with a few white lies leading the right people (including the real One) down the right rabbit holes to achieve a necessary result?
