I'd actually prefer to see a Skyward Sword prequel, incorporating the backstories of multiple different games, seeing the creation of the Fused Shadow, Majora's Mask, etc. Unfortunately, this is probably the least likeliest scenario, seeing as that Zelda is The Series Continuity Forgot.
I think we'll see a direct SS sequel if not prequel. It feels to me like Nintendo cut a lot out of SS and would probably give us a sequel with a few more upgrades to the world etc, and we all know how Nintendo loves to push the cel shaded games. Though I wouldn't like to see an SS sequel/prequel I want a totally new game and I can't see them releasing an SS sequel/prequel on the 3DS when the controls are so predicated on motion.
he worst thing Nintendo can do to me right now is give me yet another 2d Zelda game which would probably be released for the 3DS and a sequel/prequel to SS on a home console, i wouldn't enjoy that too much and i'd only be interested in figuring out where they went in the timeline, but i figure Nintendo are gonna make it public knowledge where every new game goes with each release.
I would love to see a continuation of the child timeline that implements elements from each of the games in it. I want the Twilight Realm to return. I want the Four Sword to return. I want Majora's Mask and the Fierce Deity's Mask to return. And, I want Vaati to be resurrected or reincarnated. Check out my blog for always updating details of what that (those) game(s) would look like. The Legends of The Legend of Zelda ("Four Swords Serenity of the North" and "Last Midnight Clue")
Like what a lot of others are saying, I would love to see the "Hero of Time is Defeated" timeline expanded. It holds all of the games that I grew up playing as well as the mostly "untouched" games in the series. I would love to see how the creators decide to build upon where the series originally started but continue into the future with it rather than explain the origins.
There should be a prequel to Twilight Princess. Most of the things that were there (Twilight Realm and stuff), where never given a full backstory. So Child Timeline. If the Adult Timeline should be continued to. Like telling what happened to New Hyrule. The Decline Timeline is a mystery. The games weren't really connected together, so a game connecting them all would be nice. So basically all of them.