Twilight Princess is actually my favourite Zelda game. I enjoyed the darker atmosphere, and found the level of emotion in the game to be on par with Skyward Sword <spoiler type="rot13">(Gur frpgvba jurer lbh genafcbeg Zvqan gb Mryqn, naq jura Zvqan yrnirf ng gur raq ner gjb bs gur zbfg zrzbenoyr zbzragf va nyy bs tnzvat sbe zr)</spoiler>. I also still enjoy the dungeons and boss battles, The City in The Sky, Icepeak Ruins, and Arbiters Grounds all stick out in my mind as having difficult components. I also think that combat in general peaked in that game with the number of techniques you could learn. All of that being said, it's the first Zelda game I beat, so this should be taken with a grain of salt.

I do also love the dungeons/bosses and atmosphere in Skyward Sword however, and have to agree that it is where bosses peaked.