They made some changes to the Nibelheim massacre to make it make better sense logistically, or make it more dramatic. It just ended up being stupid. Having Cloud get knocked out in the basement made sense. I just played that sequence the other day for fun and it was weird how Seph leaves the basement to go kill everyone and Cloud follows right behind him, yet the moment you get outside everyone's already dead. However, having him get injured was annoying. The slow mobility sucked. Then the crawl. Everyone is standing around Seph with guns drawn but they don't fire for a few minutes? Weird.
Also, they didn't include any quotes from Sephiroth about how he views non-Ancients as traitors. Instead, he just talks about how he's Jenova's son. I always felt the "traitor" talk was a key component of his flip. By othering non-Ancients, it allowed him to commit murders