This is called "Making Sense of the Architect's Speech".
The Cycle of the One has been broken, first by Neo himself, and later by the mistakes the Machines made in the name of Peace. In essence, there can be no return to the way things were, because the Machines simply can't do it. To explain that, let me explain a few other things that I've learned along this strange trip.
The One was the "eventuality of an anomaly", not "The Anomaly" as everyone keeps referring to him. The anomaly the Architect referred to in his speech are those that choose the real world over the Matrix (namely us. . .redpills, Awakened, w/e), something the Architect has "been unable to eliminate from what is otherwise a harmony of mathematical precision." When the Agents see Neo and refer to him as 'the' anomaly, they are simply referring to 'the' anomaly that they were likely told to watch out for.
The One was a creation of the Machines, to be used as a measure of control over the systemic anomaly (again, the .1% of the inhabitants of the pod clusters that don't accept the Matrix as real). Since they had to be given the choice, then there would always be that .1% that kept trying to wake up. The Machines knew that if that population were allowed to grow ("left unchecked"), it would spawn a civilization that would eventually rise up against them in revolution. Therefore the Machines came up with a brilliant plan, which we call the "Cycle of The One". It provided a place for the anomaly to live (Zion), a hope for a brighter future (The Prophecy), and a 'savior' to save them every so often. The Cycle was repeated often enough to keep things going smoothly.
Now, what happened that made Neo different? What caused him to choose the left door instead of the right, like he was supposed to? Trinity. Okay, what caused him to choose one over all? Love. And what caused that love to come to be? That's right, the old cookie-baker herself, the Oracle. She had been controlling Neo from the first moment they met ("And don't worry about the vase."). This time, for this One, she led him to Love, instead of Duty. Why? Purportedly, its because she wants humans and machines to live together in peace. But, who knows what the machinations of such manipulations can do to the mind of a computer program, even one as powerful as she.
So, going from here, what's going to happen? Who knows? I'd say we are going to have to consult with the Oracle again to find that out, since she seems to be holding all the cards.