I dont get the hate for the Zelda storylines. They're pretty good, even if similar main plots. But look at all the other sequels out there, they all have similar storylines to their predecesors, whether its Final Fantasy, MGS, GTA, etc...
Its part of what builds the sequel, its an ongoing struggle between two forces, and occassionally a 3rd or 4th force, but mostly 2 main people- the protagonast and antagonist.
Back on point, I feel that there's enough variance in the Zelda game stories to make them unique, going from N64 onward, OOT had the time shift of 7 years and to alter the future... Majoras Mask had a different antagonist, Wind Waker changed the world map entirely (or did it? dun dun dun!!) and Twillight Princess had several different shifts in how the world was altered, including higher level co-protagonists and co-antagonists. If anything, TP could compare best to A Link to the Past, with the dark world/light world concept, which is about a 14 year gap between games.
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