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.