1. Graphics • Reminiscent of Twilight Princess but expanded to include a wide range of colors rather than exclusively relying on shades of gray, brown, and green. Although honestly, I'll be fine with anything as long as it isn't Wind Waker / Phantom Hourglass / Spirit Tracks inspired.
2. Shady Companion • I think a more sarcastic companion with some ulterior motives forced to work with Link by external influences would be an interesting twist. Like Tatl, but even shadier. A companion that comes to mind is the Cheshire Cat from American McGee's Alice, if anyone has ever played that. The Cat will sometimes offer you explicit advice, but more often he will give you a riddle or just say something ironic instead of bashing you over the head with the solution to a puzzle.
3. Ice Area/Dungeon • This got skipped in Skyward Sword, so it's time for a comeback. For the dungeon, I might like to see Ice mixed with some other element though. I feel like Ice + Light could have interesting results.
4. Overworld • Large, interconnected, and content-filled. In fact, if it has to be smaller, I'd be okay with that as long as it is filled with content and not just empty space.
5. Items • Surprise me.
6. Gerudos/Zoras/Kokiri • I'd like to see at least one of these races/species return. I know it hasn't been that long since we've seen Zoras, but seriously... where did the Gerudos go?
7. Political Corruption • I've always been confused by how awesome this series makes hereditary monarchy seem. Surely, some of the royal family must be either useless or malicious. I would like to see more uneasiness surrounding the throne.
8. 3D Characters • I mean this in the "literary" sense - characters with multiple personality traits rather than just being boilerplate characters like are pretty much the norm in this series. (Ghirahim and Midna are example of characters that I felt were more interesting/complex than we normally see.)
9. Keep what's working • A lot of the changes in Skyward Sword were for the better. I loved the element mixing in the dungeons, the greater relevance for rupees, dialogue options, and unique puzzle elements.
10. Hydra • This is an oddly specific request, but I would love to see a giant multi-headed hydra/dragon boss where you really have to watch out from all directions and use a variety of skills to defeat each head. Orochi from Okami comes to mind.