I want to see the side quests have more of an impact on the world. Most side quests only reward is a heart piece/rupees/upgraded storage item. In Skyward Sword, the overarching side quest is collecting gratitude crystals for Beatraeux. And when finished, Skyloft becomes monster free at night. I think this is a really cool detail that can be so easily unnoticed. I want to see a few more things like this in Wii U.
I want a reward that matters. I swear, if they make the reward for the long-standing quest be rupees again I will beat someone to death. There's nothing more pointless. Most of the time, you've literally finished every other part of the game by the time you get to finishing those quests, and Rupees lost their worth long, long before then. It drives me crazy.