Graphics: Skyward Sword
We can go back and forth about the limitations of the hardware and whatnot, but Skyward Sword thumbed its nose at those limitations and came up with a very unique style. I love the painted effects.
Sound: Skyward Sword
Just plain higher quality recordings. This is nothing against Twilight Princess's music, which I enjoy very much. I also love the mysterious mood of SS's music.
Overworld: Skyward Sword
This one is a toughie. Twilight Princess arguably had more free exploring. I did love flying around on the loftwing, though, and the overworld itself felt like one big dungeon. I'm not saying I disliked TP...Zelda has always been very Metroidvania-like, so this type of gameplay always exists to a point.
Characters: Tie
Legend of Zelda always has awesome characters. My faves from TP were Rusl, Colin, Ilia, and Midna, while Skyward Sword had one of my all-time favorite Zeldas. (That is, the person.) Groose was hilarious. Ghirahim was also extremely creepy...but it put you in the mood for impaling him.
Story: Twilight Princess.
Twilight Princess was interesting in that the "princess" of the game was no longer an object of courtly love on a pedestal, but a platonic friend and equal. Link's motives for the call to adventure were very close-to-home. He had to save what was to him, his family, which included the other villagers and his girlfriend. It's nice that those familial relationships continue to be addressed through the game in a variety of ways. To me, it made TP Link one of the most grounded Links in a LoZ game, and an oddly believable, down-to-earth hero, much in the way WindWaker Link was.
Don't get me wrong, I loved Skyward Sword. It's like somebody stuck HTTYD and Inu Yasha in a blender. I also loved Zelda in that game, and she doesn't get enough screentime for being the title character, IMO. However, I'm a bit more into "down-to-earth" than "mythical", and SS really played up the mythical. That's not "bad", it's just my personal preference.
Combat: Skyward Sword
No contest. I think this is the best use of the Wiimote, ever, hands down. Sparring with the WiiU was one of the most fun video game experiences I've ever had.
Dungeons: Twilight Princess
I have Spinner bias. I loved that thing.
The only thing I disliked about it was I didn't get to use it more.
Pacing: Twilight Princess
Both games kept me on the edge of my seat, making me want to continue playing on, even when it was really time to do other things. Both games also have enough diversions to take a break from adventuring. However, I liked the minigames in TP better, so it gets the vote. I really don't know if my life was bettered at all by flailing at a stick of bamboo, and the harp-strumming thing was annoying. But snowboarding was as fun as it was frustrating.