Ok, here are my 2 cents on what happened. I've read all the posts here and my brain is swimming, sorry if its alittle confusing.
People were wondering why Morpheus and Trinity are able to handle Agents now, what I've came up with is because they have been training with Neo, even tho it is just after the first movie, you still would have plenty of time to train I would guess.
The TV Screens on the wall in the Architect Scene are all the different responses he could have said.
Consider this possibility with a Matrix beside and Matrix, all part of a bigger program? The Matrix being one program and Zion and the "real world" part of another program, instead of "A Matrix in a Matrix".
The "Choice" Neo made was to save Trinity and have Zion destroyed. This was foreshadowed in the Tribal Dance/Love Scene where Neo could have been revered by as a God, or been with Trinity, he choose her, as he did when give the Two Choices the Architect gave him.
That's all I got for now, my head hurts for thinking about this for too long. Hopefully I'll understand more in the morning.
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Official Bullshit.
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