For the Wii U, I definitely would love to see Ganondorf/Ganon return as the main villain! This time though, I'd rather see Ganon(dorf) as the only villain in the game, thus having his background story fleshed out more. In Twilight Princess, it seemed like the main focus was on Zant, rather than the Evil King. It's been years since Ganondorf went solo, that's why I want to see this happen!
As for the 3DS, if the Zelda team were deciding to make a new title rather than a remake, I wouldn't mind a bit seeing Vaati again or possibly another wizard/sorcerer type villain such as Agahnim.