I don't feel that Twilight Princess and the 3DS would be spiritually compatible. Although the 3DS can handle the game because it is up to par if not exceeding the power of the Gamecube, I don't believe that it would work has it would feel out of place.
My favorite memory is when you first step foot on Dragon Roost Island and the awesome music and atmosphere tells you that you are entering the huge world of Wind Waker.
I would say Ganondorf because my plans of world domination combined with his plans of world domination leads to mega world domination and we will rule over all of you. Mwahahahaha.
I honestly do not know if Fi will return in a following Zelda game. Maybe she will return because of how screwed up the Timeline is she might awaken from rest.
I would be willing to wait only if the game is AMAZING but if not I think Nintendo should keep the series active because in 10 years some of us won't even like Zelda anymore.
The hardest zelda dungeon for me had to be the Ancient Cistern just because with the whip puzzles and those small rooms with multiple puzzles and me clueless.