I think Skyward Sword beats Twilight Princess on every level, except in terms of dungeons. That's why I pick Skyward Sword.
I thought Twilight Princess' dungeons were bigger and better. There wasn't a single dungeon in Twilight Princess up 'till now (I just beat City in the Sky, which became my second favorite dungeon EVER in the series, behind Majora's Stone Tower Temple) that felt subpar. All dungeons felt REALLY good. I can't say the same about Skyward Sword. I didn't like the Earth Temple, for instance. It felt really short and didn't offer a real challenge. I didn't like Sandship also. I know some people consider this one of the best dungeons ever, but to me it just felt like a boring dungeon which happened to be in a very original environment, but boring to play nevertheless. Lanayru Mining Facility is a great dungeon in concept, but it just wasn't that fun to play. I appreciate the Timeshift Stones mechanics, but gameplay wise it didn't feel that compelling. So, as you can see, I had some problems with Skyward Sword dungeons. My favorites were the Fire Sanctuary, Ancient Cistern and Skykeep.
On the other hand, every Twilight Princess dungeon felt really good to play, despite the terrible controls. I'm more puzzle oriented. I don't care that much about combat. I think that's why I prefer Twilight Princess dungeons. I like a good challenge. Nowhere in Skyward Sword I could find challenges like Lakebed Temple and City In The Sky. Combat were harder in Skyward Sword, but puzzles fell on the easy side, which is very disappointing. Ancient Cistern was the hardest dungeon in Skyward Sword in my opinion and it isn't even remotely as challenging as Lakebed Temple or City In The Sky.
Skyward Sword was a breeze to play. I didn't have moments when I felt frustrated. Twilight Princess feels like a game with great dungeons and A LOT OF FILLER in between. I just didn't feel like doing anything else in that game besides beating the dungeons. I hated the fetch quests. I hated fishing. I hated the goats. I hated the stupid Goron sumo fight. I hated the whole "take this carriage safely somewhere". I hated to defeat the shadow beings. I hated playing as a wolf. I hated pretty much everything in that game, except the dungeons. The overworld is kind of empty and boring. In Skyward Sword the whole universe is a dungeon. I especially like the Eldin region. The puzzles there felt better than the Earth Temple puzzles themselves, which is something impressive. The world in Skyward Sword just feels more alive. Yes, it is pretty linear and it lacks some of the "exploration". Twilight Princess on the other hand has a more "open world", but it has nothing in it.
So, I'm still playing Twilight Princess. I will beat it pretty soon. I might change my mind, but as of now I grant victory to Skyward Sword. It was so much fun to play that game, even if Twilight Princess pretty much destroys it in the dungeon department. Dungeons are my favorite parts of any Zelda game, but the filler in Twilight Princess is SO UNBEARABLE that it loses the cake. It's just disgusting what you have to go through in TP to get to the fun parts. It is a very crippled game. Skyward Sword has less filler, even though it can be very repetitive at times (I'm talking to you Imprisoned ...).