A look into a possible restructuring of a Legend of Zelda game.
For the past few years, Legend of Zelda fans have been hoping for a change to the way that Zelda games are structured. Since the release of A Link to the Past on the Super Nintendo, most of the games have followed the format of a beginning with three dungeons, then some sort of plot reveal/twist, moving into another five to six dungeons, and finally into a small dungeon leading up to the final boss.
The exception, at least within the 3D home console entries, has been The Legend of Zelda: Majora's Mask, where the game had only four dungeons. Nintendo instead decided to focus on player interaction with the various inhabitants of the world to acquire masks that helped Link to navigate about the land. Legend of Zelda: The Wind Waker didn’t feature as many dungeons, but still followed a similar structure to A Link to the Past and Ocarina of Time.
With the release of Legend of Zelda: Twilight Princess, it had become enough for long-time fans of the series, and while it is still an enjoyable game, many started to feel the overall structure and mechanics were a bit stale.

In a lot of discussions about the structure of Zelda, making the game structure non-linear is often something people would like to see return. Or at least, having the choice of a few different dungeons to tackle that are not in a strict order. However, this is difficult to pull off. Firstly, telling the story can become difficult. Since the way you acquire items is from finding them inside the dungeons, there needs to be a set order to the way you complete the various areas, so you can move more freely across the land, and have more complex dungeon designs as you gain more abilities.
If I were to change Zelda, the first thing I would do is to take the items out of the dungeons altogether, or at least the majority of them. That way it should be possible to structure the game so you can acquire items in almost any order you want, and in turn be able to tackle multiple dungeons at any point in the game. It also allows for free-form boss designs. Most Zelda bosses require the player to use the item they find in that dungeon to defeat it. Taking the items out would force the designers to be more creative, and it would take the player longer to figure it out, as they would have to try different strategies to find out what works. Multiple items could be effective, but with some being more-so than others.
So, if we take the items out of the dungeons, where do we put them then? Some could be hidden throughout the overworld, giving you more incentive to actually explore. Others could be linked to Majora's Mask style side quests. The player would then have to interact with the non-playable characters in a more meaningful way, and this could also used as a means to tell the story.

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The problem with taking the items out of the dungeons though, is that it would be possible to run into a roadblock halfway through an area, and then the player would have to go back out and find a new item, which could frustrate some players. One way around this would be to create shorter areas to complete; think of it like Super Mario Galaxy, where a lot of the levels were bite-sized, and usually concentrated on a couple of mechanics. Some of the areas could be made in a similar way, so instead of, say, eight dungeons in the game, maybe the number could end up somewhere between 15-20, with some being smaller, more concentrated pieces of design, and others resembling the more lengthy Zelda dungeons. This would reduce the chances of someone having to keep going in and out of dungeons if they had not found enough of the items, or at least give an indication early on that they need a new item to continue.
The story conceit I came up with for this could be that at the beginning of the game, the Grand Temple, used to house the Triforce, gets separated into small pieces to protect its contents from being stolen. The temple is scattered over the land, and only by completing each of the pieces will the temple be restored and the Triforce given to the one who did it. When the temple is reconstructed, it would also provide a large final area that uses every item that the player has at their disposal.
The villain of, course, tries to restore the temple himself, and gives the world's inhabitants grief by trying to extort information/items out of them. That would give a reason for completing the side quests, and give the player tips to temple piece locations and the various tools and weapons, while also telling the story.

A lot of the game would take place out in the overworld, something which hasn't been a big part of Zelda games for many of the 3D ones. I enjoy exploring the land, but there has to be an interesting design for me to become invested in it. Having better rewards is also a key point in pushing players to find hidden nooks. These points are what drove my design idea.
Overall, Nintendo has been providing excellent Zelda games since the creation of the series. A lot of fans want Nintendo to shake up the formula with the forthcoming Skyward Sword, and hopefully they will succeed in not only changing the way the game controls, but also in changing the way the player progresses through the game. I have come up with something I think could work, and I hope Nintendo has something fantastic to surprise us with in regards to the Zelda formula.