The problem with doing a direct sequel now, though, is that they would be heavily bound by the story so far. It would be far more liberating to just create a story completely separate and independent of all other games, and then find a logical place to fit it into the timeline.
And yeah, Majora's Mask is my favorite game period (tied with Portal 2 though) - but what makes it different is that, while chronologically it is a direct sequel, it is everything that Ocarina of Time was not. Dark, character driven, haunting, mysterious. It isn't just "Ocarina of Time 2" - it is very much its own game that only shares a chronological relationship with Ocarina of Time. Phantom Hourglass is much more in the "direct sequel" route, and that is one of the reasons I did not particularly care for the game - it doesn't do too much to really distance itself from Wind Waker, and is perfectly content to wallow in Wind Waker's style and themes.
I'm not necessarily opposed to direct sequels, as long as they distance themselves and stand completely alone as their own games - and if that's the case, why should it matter if it is a sequel or not?