Entire post is sensitive for those who haven't completed it yet.

(SPOILER)Moot point here but frankly the whole "You know they let me choose" line Cortana says to Master Chief during the trilogy "You were lucky John" and "I sure know how to pick 'em" they kinda take on a new light after reach. After all, Cortana did not choose Master Chiefl, she chose Noble 6 except he chooses to stay and protect the escape of Captain Keyes and the Pillar of Autumn alone on the mass cannon since it's very much needed. This means Cortana's first choice died. Master Chief was a second or rather a forced decision not her primary choice. Now we know a lot of what Cortana tends to say is related to what is said by Dr Halsey but still talk about different stuff!