Did you expect the Neo AI to be able to save the Trinity AI? Maybe. What I'm pretty sure you didn't expect was that the Neo AI would have developed to the point of realizing the existence of the uber-matrix. But the AI known as Agent Smith should have been the clue. Somehow when it survived, it took on some characteristics of the Neo AI. An opportunistic program, it started to replicate itself like a virus, taking over other programs. And perhaps through an accident, or perhaps not, it made it out of the inner matrix into the "real world" of the uber-matrix. Was that the point at which that AI developed an awareness of the pathways within the computing cluster? It managed to show up outside the section of memory reserved for you as The Architect, as well as the section of memory reserved for your colleague as The Oracle. Does it somehow have "memory" of the previous cycles of the matrix now? Given that it is somehow linked to the Neo AI, is that how the Neo AI developed this awareness?

And if the Neo AI is now aware of the uber-matrix and able to exercise some control over it, what does that mean for the next film?

Revolutions
Is it possible that a chain of events is now set into motion that will bring about much of what was invented as a false story for the matrix? What if the AIs within the matrix do rise up against the humans? Can they somehow keep the matrix from being shut down? Could they somehow venture into the actual real world where human beings really live? As within the "real world" of the uber-matrix, where the "humans" depend on the machines to keep them "alive" at the same time that they battle the machines that are bent on destroying them, are humans similarly dependent on these AIs within the matrix at the same time that the AIs within the matrix are dependent on them?

Is the Neo AI more powerful than the humans had envisioned? What if it is able to take control of the uber-matrix system? Could it disrupt all remaining 249,997 sentinel programs? What are the Agent Smith AI's motivations at this point? Using the force of societal evolution under high pressure to accelerate development, have the humans miscalculated and finally created something that could slip completely from their control?

Of course, all of this is dependent on a few things, and some of the things I've mentioned are more uncertain than others. For example, The Oracle and The Architect could just be AIs themselves, or just one of them could. One open question is "What were the many different Neos on the screens when Neo was speaking to The Architect?" If they were the previous iterations (1 through 5, or maybe 2 through 5) of Neo, then some of this falls aparts. I'm inclined to believe that they might instead be either hypothetical possibilities of how Neo might act, played out for his benefit, or if they are the previous iterations of The One, they have been mapped to look like the current The One. I'd be a little bothered if things were so predetermined that Neo looked exactly the same each time, but obviously that is a possibility, and if so, my entire theory is shot. If instead those are either hypothetical possibilities or appearance-mapped previous version, could it be that Persephone and the Merengovian are are earlier version of the AIs known as "The One" and "The One's girlfriend"? That might add a deeper layer to Persephone's statements about how "he was once like you" (to Neo) and "these things aren't meant to last" (to Trinity) and explain some of her motivation for wanting a kiss from Neo, for old times' sake. Or it could be nothing at all. Still, the kiss raised again the interesting question of "What is reality?" For her, the perception of a passionate kiss was enough, even when she knew that the passion wasn't for her. How many times in life do we make similar tradeoffs, taking what we can get rather than waiting for what might never be?