The only way in which I can imagine whatever this mess is that you're referring to is by accounting for Before Crisis and Crisis Core and their subsequent relation to the main game. Advent Children and Dirge of Cerberus occurring after the game really bare no impact (even if they include flashbacks, Dirge in particular in its introducing the character of Grimoire Valentine whom we'd never heard of). Not having the ability to play BC, I don't know with any certainty it actually has any real impact on the main storyline. The existence of Genesis and Zack's apparent defeat of Sephiroth are huge problems for fans.

My biggest issue has always been the end of DoC which hints at the continued story of Genesis. I want that story.