All right...I saw it twice, and have been playing Enter the Matrix too. Obviously, I loved it. Great action, and definitely left you wanting more.
My theory on the whole multiple matrices idea...I think that when Smith was "destroyed" by Neo, he left a little of himself in Smith, which helped Smith become a "virus". And, when Smith tried to infect Neo, he left a little of himself in Neo. So those two are connected. That's why Neo jumped when Bane returned to Zion after being infected. And, Link even had trouble recognizing Neo's code after he leaves the chateau. So he's been changing. Maybe, since he is "The One" he can just do this...he might still be a program, but he's got some humanity in him, and he's learning.
Just my two cents.
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"Give her your coat"
"Why me?"
"Because you're perfect."
"You have a point there."
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