I've been playing the series since LttP. Twilight Princess is my top, for presentation and storytelling.

I feel like Skyward Sword tried to repeat that, but the dungeons and style / atmosphere of the world of TP still come out on top (even though I'm not very much into gothic style and furries). I think SS is way too cartoonish and happy-go-lucky for a world where the surface has been abandoned to the demons and yet everyone who lives there is cool (gorons, kiwis, moles, proto-Zora), that's a massive tonal dissonance between the narration and the actual environment and it just takes me out.

The next ones on my top list are Minish Cap and Link Between Worlds.