I don't think Nintendo should adopt a 2D top down approach with Zelda on Wii U, I think it's important they keep their handheld and home console games distinct if they want to be able to sell two lines of hardware. I also think it's better for the franchise if Zelda plays to the strength of the hardware it's on; the 60fps, top-down approach works beautifully with 3DS's stereoscopic 3D, and I think something would be lost in the transition to Wii U. That being said, I certainly don't see why there can't be top-down sections in Zelda U, perhaps they could take place on the gamepad screen?
I think what Nintendo can take from A Link Between Worlds into Zelda U is the commitment to a faster paced, far less linear Zelda that has more in common with The Legend of Zelda (1986) than it does Ocarina of Time. Narrative light, non-linear dungeon progression, side-quests and mysteries. I keep saying this when the topic comes up, but make it dangerous to go alone: if you switch off Miiverse, for example, you miss out on hints and warnings. If you keep Miiverse on, other heroes can leave messages and warnings in your game. Nothing overt, perhaps supply a basic Hylian alphabet and allow players to construct different messages from that, and perhaps use drawings. Have a choice of difficulties from the beginning. Miiverse feeds into this: use it a lot, and you have the hand-holding that Fi etc bring into Zelda, use it lightly or not at all, and you are closer to the older experience of Zelda.
With respects to story, I'd like to see Nintendo veer away from what they have been doing and what the majority of the console industry is doing: cinematic, scripted, dialogue heavy narrative. Allow me to play the story through the architecture, puzzles and monsters of the dungeons, the music, environments and mechanics of the game world. Do things with Zelda that only videogames can do. That's what made the first game so revolutionary. If the act of playing the game from moment to moment is immersive on the strength of the world, the dungeons, the enemies, the music, the mechanics, you can supply a far more powerful story than you can with written cut scenes and cinematic motion capture. Provide a story that is experienced, and not told.
Oh, and return Ganon to a mix of Twilight Princess and his early pig demon days. Something horrific and demigod esque in a flaming skull form, and some kind of genuinely huge, monsterous demon form.
