I would combine aspects of my favorite Zelda games while adding some new stuff.
* The first is the most important, an open overworld like Twilight Princess but with more in it. Think Xenoblade Chronicles, creatures roaming around, ignoring you for the most part, unless you provoke them. Beautiful landscape with wonderful music.
* A strong connection between Link and Zelda. Both Spirit Tracks and Skyward Sword demenstrated this. SS made them the best of friends and developed their friendship throughout the game. ST made her the companion, also strengthening their newfound friendship, evidenced by their holding hands at the end. I think that Zelda should once again be his companion through the game as a disembodied spirit because of some event that puts her in a coma and accompanies Link while her body is healing.
* Each boss needs more than 1 phase
* More than just one villain and a twist on the whole "hijacked by Ganon" concept. One villain could be working with Ganon only as a means to accomplish a goal of his, such as revenge against the royal family, and plots to betray Ganon. The other could be serving him, not because he's brainwashed, he's offered something in return or has been tricked, but, here's the unique part, he serves Ganon by choice. Something like the A-Squad Rangers from Power Rangers SPD, a rival of the hero, someone who is seen as the better or is more accepted by the public turns evil of their own choice, thus giving Link a more symbolic victory of overcoming what he used to be by defeating the person he was overshadowed by.
* Continuity nods and fanservice (by that I mean stuff like nod to Ocarina of Time Skyward Sword, not like, say, Zelda in a bikini)
* A supporting cast with personality as well as their own subplots and have some role in the main story, like training Link's swordsmanship or presenting the boss rush. Also, show how they change depending on what Link does. For example, Impa would start out opposing Zelda's friendship with Link like the king, but because Link is the only other person who can see her spirit and of his growth, she quickly changes her opinion on him.
* Going back to that rival thing I mentioned. A more confrontational rival than Groose, someone who is always seen more accepted by the public, humiliating Link and is praised by even the king, yet in his attempts to court Zelda, she rejects him in favor of Link.
* Like Skyward Sword, give Link a reason to go to the dungeons for MacGuffins, for example, after obtaining the Master Sword, his reasoning for visiting the dungeons would be, like The Wind Waker and Skyward Sword, to restore its power, or in this case, learn new techniques with it, like Sword Beam or causing a quake with it like in A Link to The Past.
* Like Skyward Sword, an optional love interest would be nice. In this, case let's say Malon, Ilia and Kina are secondary love interests. You could start a relationship or break off with them depending on what advantages come with them. Example, if you pick Malon you get free Lon Lon Milk and can ride Epona around the track for free to beat your record.
* Have some strong themes, in my case, themes of Idealism vs Cynicism, the underdog, relationships and growth, both physical and spiritual.
Throw in dungeons, each a different theme, fan favorite characters, iconic weapons and an excellent score and you have, what I would call, the perfect game that I could make.