I like the crazy ones. What can I say? For a long time, I slept with the script of the thing under my pillow, hoping I'd get smarter by osmosis. John inherits the dubious honor by a non-negligible margin. While W. was a chef d'oeuvre of character exploration, JJ manages to not only further the character arc, but the overall plot as well. It also makes significant use of the entire cast. This insane universe is as much about Shirley as it is about John. Chiana is no wallflower either.
Of course, the beauty of it all is that this acknowledgement of audience expectation doesn't close any door. We know that they know that we know. It doesn't change a thing. However, it appeases those who have been wondering why no one is concerned and no one is asking questions. In any case, it appeases me. It's not that John hasn't noticed or isn't worried about the odd behavior of some of his crewmates. He's simply not expressing his concerns out loud, keeping his cards close to his chest.
'There is no longer any distinction in my mind' is, in hindsight, lovely foreshadowing for an episode where John finds himself thrown into a world built from his dead twin's memories. Perhaps we find another example of meta awareness here. I wouldn't go as far as to say that reintegration occurred, although the game made reference to events this John did not know about. Instead, John tagged his own set of memories onto the game. Yet, John told himself 'You really are John Smith.' And in the end, I believe John followed a path not at all different from that of his twin. This one follows in the footsteps of the illustrious hero, albeit shaped by his individual experience and current situation.