Although I acknowledge Skyward Sword as the more difficult game, I had more difficulty with Twilight Princess. This is due to me being 10 when I first played Twilight Princess, and that it was my first Zelda game. Naturally, I had a lot of difficulty with it. Since I was already an expert at Zelda by the time I started Skyward Sword, it really wasn't all that difficult for me.
The combat is no contest. Skyward Sword is way harder. Even for enemies like Darknuts, there was a special hidden skill to deal with them easily. In Skyward Sword, enemies actually adapted, and took away a full heart, as opposed to half a heart, or a quarter heart. Skyward Sword was also more difficult when it comes to puzzles. Fi did help, but you were still, for the most part, forced to solve them on your own. The dungeons were also much more connected, so instead of solving a whole bunch of completely seperate puzzles, the whole dungeon was like one big puzzle, where everything was connected. Not only is this better dungeon design, but it was also more difficult, as you had to backtrack, and had multiple things on your mind at once.