Honestly, I think people are blowing the changes way out of proportion. The only major change is that Seph now knows the future and is trying to avert his fate and this is used mostly as a way to explain why he is taking a more active interest in Cloud and friends wherein the original he didn't really care about them at all. All the talk of alternate timelines is just wild fan speculation based on what I believe is the misinterpretation of the scene where Zack is carrying Cloud back to Midgar which was from the original (while Zack fighting the Shinra soldiers is from Crisis Core) and in no way means that he's alive in some alternate timeline (which was a hell of a leap to begin with even if Nomura is involved).