Corrected entry: When Neo comes to the Matrix in his final fight with Smith, he sees the Matrix world as the One does (The green coding). At the end, when we see a shot through his eyes looking up at Smith, he sees the way we normally do - without the green coding. (Just by viewing the shot, it is clear that we are meant to be seeing through Neo's eyes).
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Correction: First of all, it is never stated that Neo can only view the Matrix as code after becoming the One. Second of all, it is nearly impossible in a movie to see if a shot is through the character's eyes or simply from his point of view.
Andreas[DK]