[BT: This is the "old" version of this section of the essay. I do not quite like it anymore, but its points are still valid.]
Some have remarked that, when Neo meets the Architect, Neo looks surprisingly devil-like, and the Architect -- in all glowing white, patron-like -- is like God. (Even calling him "the Architect" equates him with God.) But he is not the traditional all-powerful, all-knowing Christian God. He makes mistakes, such as his previous Matrices. And he cannot foresee everything, as we will see. The Architect is more of a creator-god, father-god figure like Odin. And Neo is not the Devil-as-in-capital-E-Evil; he is the serpent, the inventor, like Loki.
Comparing Neo and the Architect to the Devil and God is an absolutely correct interpretation. But the symbolism is not so simple as good-and-evil. Read Genesis without the a priori assumption that the serpent is evil, and the serpent becomes Loki. He is the inventor god who destroys the status quo. He is the quintessential hacker.
What the Architect tells Neo is that all of Neo's activity is according to plan. Of course it is: the cycle of birth, maturity, and death repeats forever (mythologically, anyway). The fact that Loki comes along once in a while and shakes up "the system" is easily predictable (analogy: Loki equals new technology.) Also predictable is that the system fights the change Loki brings (same analogy). Also note that the Architect is not equivalent to the Matrix. The Matrix fights Neo through its "agents." The Architect is not fighting Neo. (At least, not yet. That is next.)
But then the Architect gives Neo a choice between the object of his desire and saving the human race. We must assume that the previous 5 Neos chose to save humanity. They sacrificed themselves, Christ-like, for everyone else. However, the Architect remarks that Neo #6 is different because his "object of desire" is a single, specific person whom he loves. (The Architect says previous Neos had only a general sense of affection for, er, probably those he knew in Zion.) The Architect's apparent lack of surprise about this indicates that the specific events in the cycle differ each time and are of little consequence -- all that matters is the death-and-rebirth event.
We know Neo chose the door to the object of desire. That is against the Architect's wishes. The Architect wasn't lying when he said "you can't save her" because he has arranged things so that it is basically impossible: the door from the Architect's chamber doesn't lead directly to Trinity, it leads somewhere else and Neo has to fly quite far to get her. What the Architect does not comprehend is the true love between Neo and Trinity. There is ample evidence early in the movie that their relationship is profound. When Neo kisses Persephone the depth of the love between Neo and Trinity is revealed. Their love was also a major focus in the first movie -- it is what resurrected Neo from death.
This is beyond the Architect's ability to understand. He blandly states that Neo #6 loves someone specific as if Neo had great passion for a specific kind of pasta. The Architect does not expect Neo to choose any differently than previous Neos, and just to make sure he adds that Trinity will die regardless of Neo's choice. But Neo still chooses Trinity, and he exits the Architect's chamber on an enormous plume of fire. (Note: Fire equals change. Also, the devil symbolism again, where devil equals Loki equals change. Loki is typically accompanied by fire.) Neo then proceeds to travel at godlike speed across the Matrix to save Trinity (which he does -- twice in a row).
The Architect's blase comment about Neo #6 being different is story evidence that the entire cycle is different. Neo is going to transcend everything that has come before, because really what the Architect and the rest of the machines have failed to grasp is the concept of free will. Questions of free will come up continuously throughout the movie, most pointedly during Neo's interview with the Oracle.
 The Architect is not omniscient. We are repeatedly given evidence that the Architect designs flawed universes. (That is also a clue that this one is flawed as well. That is, it won't turn out the way the Architect believes it will.) [Back]
 To all those astonished who advance theories of a Matrix-within-a-Matrix because Neo shows superhuman powers in the "real world," you should pay more attention to the relationships. Neo and Trinity's love has already caused "impossible" things to happen in the real world, i.e., two resurrections from death. [Back]