I've played my way through about two-thirds of it, I think. Got Zack and Cloud out of Nibelheim, but hadn't finished with the location formerly known as Banora. I also have a pretty good idea of how it finishes (the howls of a thousand fangirls told me it stays true to the canon story in that much, anyway). But yeah, coming back to the story ten years later and patching in a whole heap of extra details sort of fiddles with the continuity just a weenshy bit.