I really liked it. Much more than I expected.
A few thoughts...
If the world where Zion exists isn't a computer-generated simulation, that doesn't make it any less false.
There's the Gnostic idea that states the real world is entirely sprit, its God, and the physical world is a lie, an illusion, a prison for the immortal soul. {and there many such worlds/layers between our world and the true world of God}. A Gnostic's life is a journey through these false worlds whose ultimate goal is to re-unite the soul with the soul of God {hmm, like the Matrix source perhaps?}. And each false world/prison is ruled by a spirit, called an Archon {which sounds like Architect, doesn't it?}, who acts as jailor...
So its possible Neo did stop the squids in the real world, but its in no way the ultimate real world. He's just primed for Gnostic enlightenment.
Another thing, this time from Buddhism. Speakingly very generally, Buddhism is a set of rules that teaches you to free yourself from this illusory reality, to detach from it and reach ultimate understanding. It readily accepts the existence of gods and demons, and says there just as bound by the rules as mortals. And there less likely to "detach" and reach enlightment --perhaps because of their relative power in this world.
So perhpas the Gods of the Matrix, the AI's, are kinda like dieties in Buddhism... except for Agent Smith, who is now like Neo, a little more free, seeking enlightment, or power, or whatever, since this whole endeavor is a sloppy comic-book reasoned mess of different ideas and influences {and I mean that as prasie...}
Just stuff to muse over. The W. Bros. seem to be fanboys of Gnosticism, Buddhism, and skimmed over French lit theory as much as comics and kung-fu films...
I personally think Zion is in another computer-generated reality, that its a relatively pure sci-fi metahpor for Gnostic cosmology. I think the AI's are just as trapped as the humans they pretend to control. And I sure hope the Bros. W. don't drop the ball when they resolve things...