Majora's Mask is a much better sequel than Wind Waker regarding Link's arc; Wind Waker is a much better sequel than Majora's Mask regarding Ganondorf's arc. Because these are the only two characters from OoT that are in the sequels (I mean, technically the HMS and the GDT), you can see the completion of their arcs by the end of each story. This is also why PH works as a better sequel to Wind Waker than Spirit Tracks; the themes and "character arc" of WW are carried into PH in a way they are not in ST (in fact, the destruction of Hyrule at the end of WW is undone by the existence of ST, which has forever clouded my view of the WW ending).
Majora's Mask is the childhood that OoT Zelda wished for Link. It is a depressing, dark, sad childhood. But it is also a childhood filled with beautiful people whose hopes and dreams and deaths show Link an inherent spiritual beauty.
Wind Waker is Ganondorf's attempt to rebuild his lost dream: the Gerudo are gone, Hyrule is gone, and yet he still wishes to control "the wind" or whatever his poetic line was. And, in the destruction of Hyrule, Ganondorf's dream disappears (except then Spirit Tracks happens and Zelda and Link keep on keeping on...in a kingdom...called New Hyrule).
But since Link is the protagonist (and MM is a better game), Majora's Mask is the better sequel IMO.