POSSIBLE SPOILER
I may not be saying anything new here, but according to some old versions of Revolution scripts, Neo isnt using his powers outside the matrix, they are inside yet another matrix when they believe they are in the "real world." This woud also explain Agent Smith's ability to infect and control a "real world" person , who he uses to attempt to assasinate Neo in Zion, which had me more puzzled then Neo's use of powers at the end of Reloaded.
Anywho, this is definitely not a sure thing, but like I said, it does fill in alot of holes.
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