I'd like to see the ability for swords to be tempered make a return from Majora's Mask and a Link to the Past. That wasn't a huge thing, but it was cool to see how much your sword changes once its been upgraded.
Also a Magic Rod that works like it did in the original Legend of Zelda would be cool. Shooting magic beams at things ... Perhaps it could be similar to the Fire and Ice Arrows from the Wind Waker where to solve puzzles you have to switch the rod's element from either Magic (which could be like telekinesis like the dominion rod) Fire or Ice. I can definitely see that happening and in my head, the game's awesome with it!
I know the Roc's Feather has been in zelda games recently, but the Roc's Feather is an awesome item that could be really interesting to have in a 3D Zelda Title. Perhaps it will work similar to how it did in Minish Cap's Palace of Wind where you use it to jump on clouds, or it could be used with a sort of downward-thrust attack, or I don't know, it would just be interesting to see in a 3D game, alright?!
Skyward Sword already has a running system, so I don't really see the Pegasus Boots happening. But, they do have a stamina system going on, so perhaps you could upgrade your boots with the Pegasus Boots to increase your stamina/running speed/both? Not sure, but it could work.
Hmm ... I'm sure there's more items, but none I can remember off the top of my head. Although it's not really an item, I would think spells from AoL/OoT beta would be cool, not like the Din's Fire thing, but ... yeah ...