I really, really like both of them, but if I had to choose, Twilight Princess gets my vote.

Skyward Sword has better combat thanks to motion plus, but TP has the better art style and atmosphere, Midna is a way better partner than Fi, the bosses are more epic, and it delivered the true Ocarina of Time successor I'd waited years for.

I had major problems with both games.
Skyward Sword had really bad motion control integration; ultimately, I think Nintendo forgot they were meant to be fun, not challenging.
Twilight Princess was simply boring and bland with annoying dungeons; it was always "find the key in this huge area" or "find the switch in this huge area" or "find the puzzle in this huge area"... The whole game felt like I was constantly searching through needles in various haystacks. Even getting into the dungeons had stuff like "Collect ALL 37 moon tears scattered across the map in order to enter the dungeon, which you have to do in order to continue your game."

Hmmm, after that reminder. Skyward Sword for me.

I loved the Wii, but it was part of that massive gap between N64 and Switch where I didn't like new games in the Zelda franchise.

TP easily. It had better dungeons, better overworld, and better atmosphere. SS gets a lot of love for providing lore, but the art style attempts to strike a balance between cutesy and realistic that just doesn't work for me. Skyloft is a barren wasteland and all progress is linear. I play Zelda mainly for the exploration and while TP had dozens of nooks and crannies and fun things to explore, SS was a linear slog through barely populated areas. And this isn't even getting into how annoying/unresponsive the motion controls were for me. SS is the only 3D Zelda I haven't finished; I got bored halfway through and never saw a good reason to go back.

BotW > TP > OoT > WW > MM >>> SS

My vote was Twilight up until BOTW was released it was my favourite Zelda but if I am in the mood to play skyward then it becomes the better game

I liked Twilight Princess better over all but Skyward Sword had a better story and is more creative overall

Twilight Princess :
+Many iconic dungeons
+lots of new environnements
+Story/characters
+Some really great music
+Great bosses
-The damn controls omgggggggg (played on the Wii)
-The moment you have to save the carriage (yes that does need it's own negative point it was awful)
-Outside of dungeons some environnements were incredibly empty

Skyward Sword :
+One of if not best OST of the franchise
+Great story and characters too
+Great dungeons (but less than TP imo)
+Loved some of the crafting elements
-The 2nd imprisoned
-Lack of environnements
-Overworld was lacking a bit of utility as well
-Feels short

To me, TP feels like the most they could make of the Oot formula. SS was good but clearly the troubles they had during the making are showing in game. The game has only 3 generic environnements and you have to go back for the dungeons which kinda bored me a little. The dungeons were pretty originals tho, music and story were one of the greatest in the series. But still, imo SS also suffers from being the last game of the Oot formula where they wanted to make some changes but couldn't because of the Wii.

Skyward Sword definitely had some cool ideas, most of which pan out nicely, (some sequences like the one where you carry around the time-shifting crystal are genius) but as a result of having one foot in the traditional past and the other in a more progressive present it did feel like a bit of a strange halfway house at times.

Twilight Princess feels more cohesive as a result.

Well i didn't say it was really short but idk the game itself feels like it since idk.. not much happens and you go into the same areas over and over and have so many things you repeat that it feels short looking back at it.

Tough.
I actually considered Twilight Princess to be the absolute best game of all time for a long time. Meanwhile I hated Skyward Sword until I gave it a second chance months later. Then, I loved it.
Went back and played Twilight Princess on the Wii U and I didn't love it quite as much.

I can't decide (though many are just hardwired to hate Skyward Sword--and I respect that). SS is a great game with possibly the best and most coherent story. I just need to give it another try. Hopefully on the Switch.

It is a hard one. I voted TP because it feels a little more like a Zelda game.

SS took it a little too far story wise.