I think there's a few facets to this but I want to look at two, one where you create a character that's fully customizable, and the other where it's just choosing your gender and the male/female character have a set design for the most part. Another angle I thought of is choosing which...
probably b/c ganondorf's first established appearance is in OoT, the one in FSA is a reincarnation, so it needed to be after it and apparently after TP is the spot they chose
technically that's more about the placements for the oracle games since LA was always meant to be after LTTP, then it just became about if they want to retcon the oracle games in the middle of them or not
FSA's placement is annoying but it's like a "yeah let's just toss this extra game somewhere" kind of thing
downfall timeline on the other hand essentially places all of those games on a what-if scenario, which almost feels like they're making them non-canon, it's ridiculous and in a way makes...
did the same for Kid Icarus Uprising since it's the main online 3ds game I would play, and man that game kinda hurts to play, no wonder people want it remade
b/c of how condensed skyloft was and how that's where the majority of NPCs were, and also how plenty of sidequests involve interaction among the skyloft and academy characters, I can recognize nearly all of their names on the list
though this is when it comes to the town/citizen type of NPCs...