By design and overall, Wind Waker. But I'm biased towards Skyward Sword for some reason...
Never liked (nor finished) Twilight Princess.

Wind Waker or Skyward, I'm not so sure about it. TP is the weakest 3D Zelda game imo.

Opening: WW>TP>SS
Story: SS>WW>TP
Music: WW>SS>TP
Exploration: WW>SS>TP
Side quests: WW>SS>TP
Artstyle: WW>SS>TP
Link: TP>WW>SS
Dungeon Quantity: TP>SS>WW
Dungeon Quality: SS>WW>TP
Bosses: SS>TP>WW
Combat: WW>TP>SS
Difficulty: SS>TP>WW
Companion: TP>WW>SS
Arsenal: SS>WW>TP
Overall: SS>WW>TP

I love Skyward Sword, with it being my second favorite Zelda game, mostly because of the amazing dungeon quality, while I really wasn't a fan of Twilight Princess at all, with it being my least favorite Zelda.  Wind Waker is somewhere in the middle in terms of Zelda quality for me, but I still love it.

Upon reveal, I'd never thought I'd say this but Wind Waker is the better of the 3. It's fresh, stylistic, and overall different. It always kept my attention. With the other games it was like going through the motions just because that's what you're supposed to do. With wind waker the freedom you're given once you obtain the king of red lions is very refreshing. Wanna go get your ass frozen to death on an island you're not supposed to explore, go ahead. Wanna take on some cronies inside a submarine, sure. It's just overall amazing from style to gameplay.

Twilight Princess stomps in story, dungeons, music, bosses and overall epicness. Wind Waker stomps in artsyle, charm, exploration items.

Skyward Sword is not quite exceptional in any particular aspect, but overall, I think it is the most balanced quality wise. I mean, it's not a 10 in any aspect, but in almost all of them is a solid 8, maybe a 9 in some, while WW and TP has some 10s and 9, but also some 5 and 6.

I think the game prevents you from going too far away from your primary destination till you go past Forsaken Fortress for the second time. Or maybe till Tower of Gods, i'm not sure now. Anyway, the point is the game limits your freedom from the beginning as any other Zelda game. The only difference is that this time the map is filled with nonesense like enemy towers that gives you some rupees or islands that you can't fully explore until much later. It's not until you get past a huge portion of the game when the boundries are removed.

Wind Waker, the only Zelda game I love (sorry not sorry)

TP > WW >>> SS

Twilight Princess was the epic Zelda game I always wanted. My favorite Zelda in the entire series.
Wind Waker had a great art style and personality but ended a bit prematurely. It is a "good" Zelda game.
I couldn't bring myself to finish Skyward Sword.

1. Skyward Sword
2. Twilight Princess
3. Wind Weakest

I vote Link's Awakening