Majora's Mask's Mask sidequest kind of tricked me into thinking it was a longer game. The side quests were great, but I wanted more dungeons too. I also do not know how to feeel about Fierce Diety, Its like Mario 3D Land with a Stone Tanooki, its cheating. No 3-stage boss should be taken out in half a minute.
Still one of the best and most sophisticated Zelda's we'll ever see.
However I don't know if I can pick my favorite. They're all my favorites.
And how fucking awesome was it that they made Zelda an actual character in the Spirit Tracks with a personality and always stuck by Link? I never really liked Zelda in the past because she appeared so little. She was either always captured/hiding, or turned to stone. Wind Waker being an acception, but once Terra becomes Zelda, she defaults into no-personality mode. So Zelda's character in Spirit Tracks is a critical factor to why I loved Spirit Tracks so much. All the companionship of Navi with all the moe-ness of terrible anime.
Can't comment on Skyward's Zelda though she does appear to be very charming, atleast in the begginning in the game. I bet she gets kidnapped and goes into silent mode.