I too very much liked the Architect scene in Reloaded, it was about the only moment of the film I thought was actually genuinely good and seriously engaged with its own concept.

To me, it does several things at once. Firstly it provides a genuine Machine perspective on the Mayeix, and on free will itself - the remainder of an unbalanced equation. Note that this tells us that choice is real, and cannot be fully accounted for, and it does so in the least fluffy, most technically precise language one could smuggle into an action movie. Literally telling us that choice is real and cannot be entirely predicted is kinda a big deal in a movie about, you know, free will.

The second thing it does is recontextualize literally everything that happened previously as not being glorious rebellion but part of the system of control; the Matrix as a system extends far beyond the bounds of the simulation itself. The prophesied hero is just another cog in the machine; prophesy is another instrument of control. Even the One's morality is a method of control, seemingly forcing him to choose the perpetuation of the Matrix as the only moral option.

And I really love the detached delivery of all this, driving home that to the Architect this is just another Wednesday at the office. It's actually like two intelligent people talking about a complex concept, nobody yells or gets angry (except the previous TV Neos who all fundamentally failed to challenge the Matrix). It's a very different climax than the loud self actualization of the last movie, and it works fantastically for me.