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.

Twilight Princess is its atmosphere, though–it's just not the one that Skyward Sword is. Skyward Sword has more compact dungeons, sure, but I actually found them to be easier than Twilight Princess's. Sure, Twilight Princess is pretty big and a bit empty at times, but I feel this is just a setting thing. (Skyward Sword's overworld is kind of a weaker, larger dungeon to be honest.)

> Skyward Sword's overworld is kind of a weaker, larger dungeon to be honest.

Notably, if you read interviews with the developers, this is precisely what they were going for with the overworld.

It was a great idea that didn't pan out because, for whatever reason, the over-world areas simply weren't as well designed as the real dungeons. Fi interrupting you every 30 seconds didn't help either, of course.

At least Fi is no Navi ;)