well from what I remember, it doesn't change the story that much. When you get to asgard after mephisto mission, nick fury talks about how sad it was to lose one of the x-men. Also if you save nightcrawler, In the original unmodded version, mystique takes her wrath out on prof x for the death of her son, and at the profs funeral they show nightcrawler standing there lol. It must have been something that the programers didn't realise. But I think they cut the out parts of the end when you use magneto, where uatu states what you did and didn't do. But I don't exactly remember.