In comparison I felt that Twilight Princess had a stronger world, music, dungeons, more inspired bosses overall. Skyward Sword's worlds felt a bit lacking, especially with almost no appearance of an ice area, the dungeons felt unfulfilling until the Fire Sanctuary in that they felt like 5-8 large rooms, and some of the bosses seemed kind of lame, especially the one on the pirate ship.
However, Skyward Sword does possess my favorite song in the Zelda series which is the main theme. The reason is that the musical genius to make such a song, to me, is jawdroppingly outstanding since the main theme when played backwards is Zelda's Lullaby. It also had possibly the best mechanic seen in any Zelda game which were the timestones and I felt the presentation, cleverness, and execution were done brilliantly.
I would say I'd prefer Twilight Princess
slightly over Skyward Sword, they're both great games but I suppose only one of them can come out on top. (Still an Ocarina of Time/ Windwaker guy myself
)