I'm going with Skyward Sword as the better out of the two games here. First off, I'd like to state that both of these games dissapointed me, especially Skyward Sword from all the hype it created. Skyward Sword caters to a very specific gamer, sort of like Majora's Mask, and the game strayed far away from the traditional Zelda standard. Change isn't bad, but I didn't care for the direction Nintendo chose to go with this game. That being said, it doesn't lose to the complete crapshoot (IMO) that is Twilight Princess. I'm simply going to focus on what I hated in Twilight Princess rather than analyzing Skyward Sword because I feel like I've done that ten times already on this forum.
My biggest beef with Twilight Princess is the overworld. I like the idea of a large surface to explore, don't get me wrong, but the only thing to explore in that world was grass. Literally, there was nothing in the overworld. God forbid if you didn't call epona because than you were really screwed. It took ten years to get from point A to point B, and they didn't give you anything to do in between! Either condense the size of the overworld so it doesn't take forever to get from town to town, or put connecting, small villages inbetween the major villages to give me something to stop by and do.
The story also peeved me off. People don't realize that The Wind Waker had a more articulate, immersive, emotional story than Twilight Princess soley because they see how The Wind Waker looks and automatically sums it up as a dumbed down game. Twilight Princesses' story was dull and shallow. They spend all this time building up Zant as a evil, intense character, and than they just blow him off in the end of the game like he was never there. I will never understand why Nintendo spent more than half the game to create such well-rounded, believable antagonist only to throw him away.
The tears of light quests also put a thorn in my spine. If they were not so long, boring, and repetitive, than maybe I would have enjoyed them. The biggest negative towards them was their length and repetitiveness, since whether or not they were "boring" is a matter of opinion. They gave you nothing to look at while you spent a half an hour collecting these tears. It was a naked fetchquest that should have had serious rework. I understand why you had to do them, and admittedly, that's what got me through this horrible experience because I was motivated to restore light to the respective areas, but they were executed so poorly it hurt. It also added an uneccesary amount of linearity to the game since you couldn't backtrack once you entered the twilight realm.
Now, you may be arguing that Skyward Sword had the Silent Realm, which was similar to Twilight Princess' tears of light quest, but they were different in one key point of you ask me. The Silent Realm quests were significantly shorter than the tears of light quest. Now, it was flawed since you only had one chance to get hit, but most of them were pretty easy that it only took two, perhaps three tries. It also added the adreniline factor since it was timed, making it more enjoyable and easyer to get through.
Now, Skyward Sword is not without its flaws as well. The overworld, main quest, and sidequests all agitated me, but it was a solid game nonetheless. Twilight Princess just had so many major flaws that stop me from enjoying that game. The only thing I actually liked about that game were the puzzles and dungeons, which isn't much.