It is "complicated" or a "clusterf*ck" because the entire (or at least most of it) Zelda lore is an afterthought. Treating lore and story secondary works fine for a single game, or perhaps even two or three, but after nearly 20 games it is bound to fail with a lot of holes and contradictions. One obvious error is how Skyward Sword established that all Links share the "spirit of the hero", but for some reason Link can talk to himself in Twilight Princess (Hero's Shade). Perhaps it is me who has misunderstood this massively, but the point is that the holes are many, and that is the result of Nintendo not taking the lore/story seriously.
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