These following are not my ideas. I copied and pasted from another site. But, I thought they were very interesting and wanted to share the ideas............
Neo is a machine, kinda. He is a human with enhanced genetics, enhanced implants, and a machine programmed mind (probably based on a "The One" template program). That's why, at the end of Revolutions, when his body is being taken away, he is shown as an orange glow. The orange glow is how the machines see each other, and therefore how they see Neo. It is also how Neo sees Smith inside Bane... he is seeing the machine program of Smith inside Bane's mind, and therefore it is an orange glow in the shape of the Smith.
But the orange glow isn't the only reason to believe Neo is a machine. Throughout the trilogy other hints are given, such as: "His neural kinetics are way above normal.", "He's a machine.", " Your five predecessors were by design based on a similar predication...", etc.
So if Neo is a machine, why was he created (as all machines must have a purpose)? He was created by the Oracle and the Architect to be The One. As the Architect explains to him: "Your life is the sum of a remainder of an unbalanced equation inherent to the programming of the Matrix... Your five predecessors were by design based on a similar predication, a contingent affirmation that was meant to create a profound attachment to the rest of your species, facilitating the function of The One... The function of The One is now to return to the Source, allowing a temporary dissemination of the code you carry, reinserting the prime program."
Translated, the Architect is explaining that Neo was designed to be a religious figure to the freed humans, thus causing them to put their faith (hope) in Neo and to rally around him ("...sum of a remainder...". This helps to ensure that the freed humans are focused on Neo instead of war, and to keep them all together in one place, Zion (which was built by the machines for this purpose also). Neo is a form of control in the real world.
And just to make sure that Neo carries out his part of their plan, the machines programmed him with "... a contingent affirmation that was meant to create a profound attachment to the [humans]." This, along with his enhanced abilities and the "guidance" of the Oracle, keeps him on the intended course.
The Architect also states that "The function of The One is now to return to the Source, allowing a temporary dissemination of the code you carry, reinserting the prime program." This simply means that The One program in Neo's mind is the most important (prime) program in the Matrix, and that now that his mission (purpose) is complete, he must return to the source for deletion (all machines must have a purpose). The phrase "... temporary dissemination..." means that the The One program will be used again in the next version of the Matrix. This is also why Neo's choice of the left door will destroy the Matrix, as there can be only one The One in the Matrix at any time. By staying in the Matrix Neo is preventing it from being reloaded, as a reload will do nothing without another The One for the next version. (In programming terms he is the highest priority task, and he will not release the Matrix program's main semaphore.)
OK, so The One is a human with enhanced genetics, enhanced implants, and a machine programmed mind, and was created by the Oracle and the Architect to carry out a specific purpose (form of control in and out of the Matrix) in each iteration of the Matrix. Now let's see how The One fits in with the entire story of the trilogy.
As is explained, the Matrix was created by the Architect, at the end of the war with the humans, as a way to control the humans and use them as a power source (I know, hard to believe...). The first Matrix was "... quite naturally perfect, it was a work of art, flawless, sublime.", while the second Matrix was redesigned "... to more accurately reflect the varying grotesqueries of your nature." Basically Heaven and then Hell. In both cases, however, no conscious choice was given to the humans as to whether or not they wanted to believe in the reality of the Matrix. This caused the majority of humans to reject the Matrix and die (" ... whole crops were lost.".
To solve this problem the Oracle was created, and realized correctly that the humans needed to be given a choice: " Thus, the answer was stumbled upon by another, an intuitive program, initially created to investigate certain aspects of the human psyche... she stumbled upon a solution whereby nearly 99.9% of all test subjects accepted the program, as long as they were given a choice, even if they were only aware of the choice at a near unconscious level." So by giving humans a choice, even at an unconscious level that only 0.1% are ever aware of, they accepted the Matrix.
Unfortunately for the machines, however, a majority of the 0.1% who were aware of the choice usually chose the real world over the Matrix. "While this answer functioned, it was obviously fundamentally flawed, thus creating the otherwise contradictory systemic anomaly, that if left unchecked might threaten the system itself. Ergo, those that refused the program, while a minority, if unchecked, would constitute an escalating probability of disaster." The machines therefore also needed a way to control the 0.1% of the humans who chose the real world over the Matrix, thus Zion and The One were created.
As was explained earlier, Zion was built by the machines to ensure that the freed humans would all gather in one place, and The One was created to be their religious figure, helping to distract them from renewed war with the machines. Both forms of control.
But even with Zion and The One, the unpredictability of choice ("systemic anomaly" still forced the machines to occasionally "reload" the Matrix. This always occurs when The One reaches the Source, which he can only do after attaining the level of power necessary for him to defeat the Merovingian, obtain the Key maker, etc. The One program is then temporarily reinserted into the Source (machine mainframe), in preparation for the next iteration of the Matrix. In the process the machines gain the knowledge and experiences of The One, allowing them to better predict the future behavior of the humans, and thus reduce the systemic anomalies.
So that is the situation at the start of the sixth iteration of the choice-Matrix. Luckily for the humans, however, the Oracle does not want them to be enslaved in the Matrix any longer, or for the freed humans to be killed. She therefore decides to take a risk and use Neo to bring about a " revolution".
In M1 (The Matrix) she meets with The One, Neo, as she has done in the five previous iterations of the Matrix. Normally she simply helps guide The One to his meeting with the Architect. Except this time the Oracle gives Neo a special cookie, which he eats. The cookie isn't actually a cookie, though; it's an upgrade to Neo's program. Since the Oracle created the The One program, she can predict exactly what Neo will do in the future, specifically how he will destroy Smith (from the inside, with some copying from Neo to Smith occurring). She therefore includes in the program upgrade code that will give Smith the ability to replicate himself, and for Neo and Smith to see the future as she does.
