M1 goes out of its way multiple times to establish the fact that Neo perceives time in slow motion. In other words, he doesn't just have quick reactions - he literally has the reactions of a machine. How else could he turn a corner faster than fire from an explosion can? This is critical to understand in order to fully accept the scientific explanation behind Neo's ability to communicate wirelessly with the Source (see Neo's Powers: Stop Sentinels).
The following quotes all seem insignificant when watching the movies (most hardly notice the quotes), but taken all together, it becomes very clear that Neo's quickness of thought is a very significant fact that the movies are seeking to establish:
Morpheus: How is he?
Tank: Ten hours straight. He's a machine. (M1) Mouse: Jesus Christ, he's fast. Take a look at his neural-kinetics, they're way above normal. (M1) Agent Brown: Only human. (M1) [This also shows that other machines/programs knew Neo was the One before Neo did. They could probably "see" it in Neo's code.] Trinity: How did you do that?
Neo: Do what?
Trinity: You moved like they do. I've never seen anyone move that fast. (M1) Neo: I just haven't been able to sleep much.
Councillor Hamman: It's a good sign.
Neo: Of what?
Councillor Hamman: That you are, in fact, still human. Agents: Do we proceed? Yes. He is still... only human. (M2) Merovingian: You see, He's just a man. (M2)
In the first quote, Tank is so overwhelmed by the amount of data Neo can digest in one day that he cannot express it other than to say Neo is a machine. Tank has no idea just how right he is. The second quote seals it for good: Mouse gives us an official measured comparison of Neo's reaction time vs. other humans. And, in case there was any doubt in your mind whatsoever about Neo's mind, Trinity confirms that Neo moves just like a machine would move. Even Councillor Hamann, a man who hasn't even seen Neo in action, has apparently considered the possibility that Neo isn't human.
The Agent Brown quote and the last two quotes confirm that even machines must constantly give themselves "comfort reminders" that Neo is technically human. Unfortunately for them, it is just a technicality that doesn't do machines much good when fighting with Neo.
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