Tough call. For me I'd say Skyward Sword - I just enjoyed it more! Heard negative things about the motion controls before playing it but I think they really add to the overall experience. The combat is unique to any game I've experienced in gaming anywhere. I also think the dungeons were awesome, the pirate one in particular was really cool. It does have a weaker overworld but that's the only real negative I can think of.

I liked Skyward sword more, but consider Twilight princess a better Zelda-game, if that make any sense.

The Zelda formula is almost perfect in Twilight princess, the only thing I really miss is a better use of items, some of them are way underused.
Skyward sword was my most enjoyed playthrough of just about any game. Even so, I can name a lot more things I did not like with it compared to TP. But the feeling I got playing SS trumfs TP.

Funny thing, I own both games and I haven't played either. Huh.

Probably the two weakest 3D Zelda games imo, but I think TP is the better one.

Indeed. Wind Waker and Breath pf the Wild are so much better.

Skyward Sword because of the prequel narrative, finding out about the old gods and Demise was fascinating. Plus the impressionist art style was beautiful and unique.

2 of my favorite games, both with some of the best dungeons in the series. I now find TP to have aged a bit due to how slow Link moves as well as a couple of clunky sections early on, as well as the graphics and midi music. Skyward Sword is my favorite game ever. Awesome controls, great characters, and great gameplay.

Both are great games, and better than Ocarina of Time.

I give the nod to Twilight Princess though. It is basically "Ocarina of Time 2" and improves on many things that made Ocarina itself a mid tier Zelda game.

If you are looking for a challenge though, Skyward Sword is the harder game. Not because of bad controls or anything, the motion controls worked great. It is just structured to be a more difficult experience than past Zelda games.

Twilight Princess has better dungeons, better bosses, far more interesting items, a best sense of escale for its world and a cooler setting thanks to the whole Twilight Realm/sense of doom and despair that the game constantly throws at you. Majora's Mask kinda does that, but I think Twilight Princess excells at it thanks to its unfairly infamous tutorial. It helps to create a bond with the people of Ordon. We care about them. And then... shit goes waaaay south. It sets the tone for one of the darker Zelda games.

Skyward Sword has a more vibrant art style, better and more original music, a very cool upgrade system for items and potions, better sidequests, better characters and while the world was more linear, it was far more alive. And, while TP is a very good take on a darker Zelda, Skyward Sword is just as good... for a classic Zelda setting. The relationship between Link and Zelda is the best we have gotten yet, seeing how everything about the Triforce, the hero, the goddess and the demon king began... the very early steps of the land of Hyrule... all of that makes for a great tale that I enjoyed form start to end.

All in all, I think that both are excellent games for different reasons. Maybe I would go with Twilight Princess because it was my first 3D Zelda and the nostalgia is strong with it. But being objective, I think of both as equals in terms of quality.

Twilight Princess easily, I consider it one of the best of the franchise and its very strong in every individual aspect. Skyward Sword on the hand is in the exact opposite spectrum for me, Its one of the Zelda games I like and enjoy the least - which is not saying much either way, most games of the franchise are great.