In the original The Legend of Zelda: Wind Waker for the GameCube, Link was given a device called the Tingle Tuner, which allowed a player to control Tingle and help with various quests in the game. This was done by linking a Game Boy Advance to the GameCube.
Zelda producer, Eiji Aonuma, was asked why the developer decided against using the 3DS in a similar way and he responded by saying the team wanted to focus on the social aspect of Miiverse, and enable players from all corners of the world help each other. The Tingle Tuner has been replaced with the "Tingle Bottle", allowing players to write messages and pop them into a bottle and send it off, only to be picked up by another player.
The Tingle Tuner was also capable of obtaining information about a current area, and uncovering secrets. We assume there will be other ways of utilising this elsewhere.
For more details on the upcoming Wii U title, Aonuma shared his thoughts in this The Legend of Zelda: Wind Waker HD developer session.