Fierce Diety Link's power is hard to quantify without a whole lot of defined power levels in the Zelda world or even the ability to draw a proper comparison between Majora's power and FD Link's, but regardless I'm still inclined to default to Samus if only including main characters simply due to her technological advantage. If not limited to main characters, Giygas seems to be a competitor but I don't know much about his specifics. TTYD's Shadow Queen also deserves mention.
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