Equiliribirum was a great movie, but it's not very much like The Matrix at all, IMO. They have the action / philosophy thing, but they're still almost nothing alike.
You seem to also be forgetting, in your comments about Reloaded, that it's only part 2 of 3 movies. There's one more movie to go, and it will explain almost everything, I'm sure. Something tells me Neo isn't using his powers outside of the Matrix. :-P
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