Yeah, I think that actually happened in every Matrix previous to this one too, so I doubt that has much to do with it. I know that Agent Smith is vital to the plot, but I don't think anything differently happened with Smith this time that didn't any other time, unless of course Neo didn't become The One in any of the other ones, which I'm pretty sure he did...
Maybe I am off basis with your thinking though, so explain if you could.
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