I was thinking about this after my second viewing - and came to the conclusion that most of the TOS episodes could still pretty much take place as they did even with the changes that took place in this movie. A few, mostly that delt with the character's pasts, would be most effected. The events of "Where No Man Has gone Before" would be changed, as Gary Mitchell is not in the equation, although the events are not precluded from occuring. "Shore Leave"'s Finnegan would be changed as well ("Cupcake", maybe?) The biggest change would be for "Amok Time", for obvious reasons. Actually, the new circumstances might add to that story, in that Spock's pre-arranged marriage is now all important for Vulcans in their depleted state, and throw in the Spock-Uhura relationship. This could lead to the Spock-Sarek animosity that comes to the fore in "Journey to Babel". That ep changes as well, due to Amanda. Another character (Kirk maybe?) would have to tweak Spock's conscience. "The Cage" could have happened before these events, maybe Pike and Spock visited Talos IV prior, and Pike's accident, depicted in "The Menagerie" is still to occur. As time goes on, the difference between the two timelines seems to become less and less, so that by the time of TNG and DS9, they could be almost indistinguishable from the original, maybe with just minor differences. The universe has not been changed all that much, at least if you look at it that way.