»Few arguments agains THE SYSTEM THEORY«

Hi all,
Although I agree that the System Theory is amazing (congratulations to its
author) I have some points against it. I would like to hear from you guys about
these points :

1) the Author of System Theory points that the very purpose of the entire system
is to let a real artificial intelligence be born. It suggests that all the inteliggence
we see inside the System are not "real", I mean, cannot be considered inteliggence,
which is an absurd. We just have to check the intelligence of Architect, the intelligence of Oracle, Meronvigian, and so on. So it is suggested that a real intelligence would be in a virtual human that has free will. So the theory is not about the born of a aritifical intelligence, but the aritificial free will. That would make more sense.

2) The author points that a possible end for the trilogy will be Neo choosing to stay
in the system for the sake of his friends. If it realizes that all is artificial inside there, and he is the main goal of the system, why it would be so worry about the system final shutdown ? He could reprogram it if he wants.

3) Why the W.Brothers would care about the fight between Smith and Neo in M3, if
neo is about to discover that he is just a developing code , and everything that happens has that purpose ? Fighting Smith would improve Neo's intelligence at all ?

These are for start. I hope I get some replies on this. Thanks