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Drawing from a successful formula wouldn't be a Ganondorf shoo-in at the very end.
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They introduced him to the game's narrative about halfway through with the flashback, didn't they?
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And I get that the triad of forest/fire/water gives a variety of locales while also providing some 'learn the ropes' stuff as you go on, but is it really necessary to echo it post-Master Sword just like Ocarina of Time?
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I thought this was where they branched away the most. Locales like Snowpeak and the Mansion, the Temple of Time, the Palace of Twilight, weren't those stark contrasts from the basic elemental temples that Ocarina used?