Best Controls
Skyward Sword
Skyward Sword has possibly the most controversial control scheme in Zelda history, requiring precise motion controls. Apparently, this paid off. Skyward Sword's controls are arguably the game's best feature, breathing new life into the Zelda formula by changing how everything is done without necessarily reinventing the wheel. As the culmination of half a decade of Nintendo's focus on motion controls, the game was arguably the first title to really show what motion control is capable of.
Runner-Up: Wind Waker
Best Combat
Skyward Sword
Skyward Sword's controls also strongly influenced how combat was affected. Built upon the formula created by Ocarina of Time, Skyward Sword added enemies that require not only the right strategy but also the skill to defeat. Even common enemies could require thought to defeat, as they would deflect your blows with blades and shields. And of course, special items were also tied into combat, such as the whip and bow.
Runner-Up: Wind Waker
Best Exploration
Ocarina of Time
This was actually a pretty close category, but the winner was Ocarina of Time. The way the game easily transitioned between overworld, towns, and dungeons, while still making the distinctions clear, made exploring exciting and simple. Seeing the world across two time periods lent a feeling of seeing familiar things in an all-new light. And of course, the game just felt like a full world, worthy of exploration.
Runner-Ups: The Legend of Zelda NES, A Link Between Worlds
Best Puzzles
Skyward Sword
This is another instance where Skyward Sword's unique controls lent to its success. No other game in the series could do what this entry did with its puzzles. For a simple example, look up at that image. That would literally be impoosible to accurately recreate on, say, the GameCube. And that was one of the things that made Skyward Sword's puzzles so good. They showed both innovation from the new control scheme and the years of experience the developers had making these games.
Runner-Ups: Twilight Princess, A Link Between Worlds
Best Items
Ocarina of Time
When you get down to it, Ocarina of Time had all of the items you really need in a Zelda game. You had your bombs, boomerang, bow and four flavors of arrows, a hookshot, a hammer, etc. You alsoi got weird items like bombchus and the Lens of Truth that made the game more interesting to play. And of course, you also have the famous Ocarina of Time itself, and everything it has to offer. Honestly, I can't think of any item that would have made the game any better. That's a good sign right there.
Runner-Ups: Syward Sword, Twilight Princess
Best Bosses
Twilight Princess
In retrospect, Twilight Princess might have been a wee bit overrated back in 2006. Don't get me wrong, it's by no means a bad game! But look how few categories it's won! Well, this is not those other categories. Twilight Princess had EPC BOSS FIGHTS. With the possible exception of one of the Final Boss phases, I don't think there's a disappointing member of this pantheon of pain. I mean, look at that thing! I just randomly picked one Twilight Princess boss out of a hat, and got one of the most revered encounters in series history!
Runner-Up: Ocarina of Time
Best Overall Gameplay
Skyward Sword
Based on the above four categories, the VGChartz community seems to think that Skyward Sword has the best gameplay in the series. The cControls and Combat are the stars of the show, but virtually every aspect of the gameplay (save for Exploration) is respected. Skyward Sword sought to reinvent how Zelda was played. I think this counts as a success.
Runner-Up: Ocarina of Time
