Well, the most obvious change would be Kirk's death. He should have died heroically on the bridge of a starship saving everyone. Ironically, George Kirk's death at the beginning of Star Trek 2009 is exactly how I would have wanted Kirk to die, heroic self-sacrifice while commanding a starship. Instead, he dies pathetically with only one other person around, who buries him in a shallow grave on a barren planet, and never mentions him again. He didn't even get the honor of a Starfleet military funeral like Spock did in WOK or Pike in STID. And the worst part of it is that the death of James T. Kirk is treating almost as an afterthought in the film. It was disrespectful to such an iconic character (even Malcolm McDowell thinks so).