Obviously, as you said it a lot of it is just subjective, different strokes for different folks and what-not.
Ocarina of Time is still primarily seen by the largest portion of fans out there as the best Zelda game.
That said, Wind Waker is my personal favorite- but I do think Majora's Mask was the best game of the series. Did the most of having a consistent theme of healing, as well as what wounded the world around it. With this came a more mature atmosphere around you, while keeping that sort of classic adventure status. The time limit, combined with the moon above you at all times (except dungeons) instilled this sense of foreboding doom and it genuinely unnerved me- knowing it was there the other time. Overall felt much more like an old dark fairy tale. Something that appeals to kids and the young at heart but doesn't really pander to them, coddling them with things theyre supposed to be too young to understand. Or at least, that's how I felt when I was 12-13 and playing it.
On top of that, kept all the visual elements that made Ocarina of Time great, improving on many and had the intuitive system of masks that both physically and metaphorically 'masked' Link, allowing him new abilities or entirely different attributes, what with the Deku Scrub, Goron and Zora masks.
Just a great sequel, a direct sequel too, I might add.