If I were Neo, I woulda not chosen. I woulda just sat there w/ the architect forever...
After seeing it again, the people of Zion are the 1% who fail to accept the matrix. They're contained within Zion, a backup matrix. The Oracle stumbled upon a solution where if they thought they had escaped, they wouldn't ever realize tehre was another world on top of the fake matrix.
The Oracle is a program. Everything in the Matrix is a program. This also implies that the Architect is a program designed to facilitate the reloading of the Matrix. Also, the machines still obviously need humans or else they would just destroy all of us without going through this the one bullsh1t. So my guess is they're trying to figure out a way to build a perfect matrix which contains all minds and also has no anomaly in it.
What I think is supposed to happen is Neo is supposed to rebuild the Matrix. Since he can hack it, he recreates it w/ new parameters and makes it more secure this time. He becomes the Architect and effectively creates a system he can't hack, thus evolving the Matrix. He creates a software program in his likeness to act as the Architect and this fail safe mechanism to wait for a future evolution of himself to come and rebuild a better Matrix. The problem with this is the Anomaly, himself, will keep propagating through the system until he builds a Matrix secure enough to contain himself, at which point the Matrix will be perfect. Thus, the cycle continues until he picks the other door(trinity) and Zion is destroyed. Since he picks the Trinity, he will never become the architect again, because he has now chosen the matrix. He has effectively created a system which contains himself. He has gone back to the Matrix.
I dont now where it goes from here though...