Okay, I skipped a few agreements and disagreements that followed this ...
I'd say Wind Waker, as a whole, has more 'potential' than Majora's mask.
The plot strikes a perfect balance between the epic battle of good vs evil, a brilliant adventure and a character piece (not that the moon hitting the planet isnt epic, but Majora's Mask story suceeds BRILLIANTLY due to its characters).... The setting is brilliant as well; a wild, endless ocean, it's bright, vibrant, the feeling when you first get on that boat is brilliant. It's a fun, exciting, bold, fresh adventure, which is just what Zelda should be. For me it's the only game that made Ganondorf actually an interesting villain, every other one he's just 'I WILL CONQUER RAWRRR' whereas here he's already conquered, lost it all, and wants it back. Okay, there's not really any more motivation, but there's a hell of a lot more nuance to it.
Yet, somewhere, it does stumble. Perhaps too long going back and forth on the boat, or not quite enough dungeons, but that epic feeling of adventure does dwindle as you go along. On the other hand Majora's Mask only gets better as you probe deeper into it. It's a smaller game but its bursting with content.
So i'd say MM gets far closer to its full potential than Wind Waker does, but there are moments in Wind Waker that are the best the series has to offer.