In an interview with the UK's Official Nintendo Magazine, Legend of Zelda: Skyward Sword producer Eiji Aonuma said that he believes the controls for Skyward Sword will become a fundamental component of the series in the future. In other words, we're never going to play Zelda with a joystick and buttons again.
"I honestly think we cannot go back to button controls now, so I think that these controls will be used in future Zelda titles, too."
Interestingly, Aonuma thought about scrapping the motion controls altogether during Skyward Sword's development, but he's apparently now committed to form. Obviously his statement isn't definitive, but Aonuma has played a lead role in developing the Zelda series since Majora's Mask, so I'd expect to see more motion controls in Link's future.