Reposting what I said in the Halo 4 story thread in case anyone wants to discuss it.
In response to the Librarian gene song scene:
I think you're sort of missing the point as to why so many fans of the lore take issue with that scene over others.
It's the implications on the Master Chief as a character, the existence of Cortana, and all of their accomplishments.
John is set up very thoroughly in the novel The Fall of Reach, as well as the game Halo 3, as a man who has faced and overcome an incredible amount of hardship to become a shining beacon, a hero of humanity. Kidnapped as a child, put through impossibly rigorous training, barely surviving experimental augmentations - these were the cause - and winning the toughest battles, stopping multiple Halos, severing the head of the Covenant and ending the war - effects. Cortana as his partner describes him as special. Not the fastest or strongest, but the luckiest. Always pulling through adversity against all odds. This defined his character and created someone who players could place themselves in the shoes of. Someone more believable and likable, even if the slightest more human just because he wasn't truly the best at anything.
The concept of predestination introduced by Halo 4 directly conflict with 343's attempt at exploring the humanity of tue Chief, and the potential of Cortana's humanity. What significance do their choices hold, what characteristics make them human or human-like, how could they ever be related to if all they do is an eventuality rather than luck created by free will? I feel my desire to be the Chief fade because to me, that is no longer a human characteristic, but instead a mechanic to progress the story and facilitate things not conceived by the minds who originally brought him to life.
Hopefully you don't turn around and dismiss my feelings as nitpicking, because I know I'm not alone in this sentiment. What exactly he was predestined to do doesn't matter, because any predestination removes the feeling that he or Cortana have earned anything they had done in the greater context of the universe.