I am LOVING what this game has thrown at me so far, and I hope that Nintendo builds on this direction. However, there are a few ideas that I would love to see in future LOZ entries:
I wish the sidequests drew more inspiration from Link's Awakening, rather than Ocarina Of Time. That is to say that I wish they were more like the Item Trade and Secret Seashells than Gold Skulltulas. There were 26 seashells, but you needed 20 to complete that part of the game, and the reward made it worth the player's while. The Item Trade opened new possibilities in the game. I don't really want to collect 100 or 900 of anything as a sidequest, because that can become too much "filler", but with the seashells, there were just enough to make it fun, and not too much to make it feel a chore. This sentiment is all the more understandable, when one compares the rewards for 100 Gold Skulltulas VS the Secret Seashells.
For Me, 7 or 8 dungeons is the sweet spot - Minish Cap always felt one or 2 short of handheld perfection. I would've liked to see some of the shrine ideas combined to make one dungeon, rather than over 100. For me, anything less than 7 or 8 feels a little short. On that note - Remember at E3 2014, when Aonuma talked about defined exits in previous games!? Defined dungeon entrances is another convention which could be broken. Imagine the ground opening under your feet and falling into a trap, which turned out to be an underground dungeon, or under a town (in sewers, or a labyrinthine castle/mansion basement). If it was a trap, you didn't go through the entrance - Instead, your objective would be to explore, and ultimately, escape. So, it would be a "reverse dungeon". The Guardian could be waiting for you at the way out, or you could face it in multiple areas before that point.
Caves!! A Link To The Past had them. Link's Awakening used them as Moblin hideouts and mazes leading to Eagle's Tower and Turtle Rock.. I feel that shrine ideas could be integrated here, too, instead of having hundreds all over the place.
More Cities/Towns/Villages!! Poorer areas, richer areas, differences in lifestyle, technology, nightlife, town events (for example, carnivals, circuses, festivals, etc.).
I also hope that motion control support returns as an option. After playing LOZ: Skyward Sword and Twilight Princess on the Wii, I feel that "Press A for swordplay" can be a step back.