Well, since Majora's Mask is my favorite game, I think the answer is quite obvious for me.

The Wind Waker explains what happened to Hyrule after the Hero of Time left, but it never tells what happened to the hero itself. Although the ending of Majora's Mask is open-ended, it tells what happened to Link along the way. Also, just the fact that it's the same Link as OoT Link seems to make it a more relevant sequel, in my opinion.

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Meh