Neo rejected that part of the knowledge the Architect imparted on him, calling it "bull****". In turn, the Architect described Neo's reactions as "denial" and "hope", showing contempt toward both.
The sequel took the side of hope, starting with the Oracle mocking the Architect's ability to predict anything. And then Neo saved both the Matrix and Zion.
And yes, my knee-jerk response to this was and still is: Damn those trolley-cheating protagonists! Heck, Neo's victory was made possible by something literally called the Deux Ex Machina.
Unless the Wachowskis never truly let go of the original pitch with the Matrix providing processing power. In which case the path the Machines went on was all about human thinking.That requires a human biology and human-ish upbringing, which doesn't seem to have been the path the Machines went on when they started creating their own AI.
And I still find that theory, in one word, boring.
We had just been told how Zion was built on a lie to serve as another level of control, all this in a way that did not require the post-apocalyptic Earth to be literally part of the Matrix. Excessive verbiage aside, I thought that was brilliant.
But nooo, the fans went all "Ah, they must still be plugged in".