I only really had two problems with the motion controls in SS. The first being using the bow, especially in the pumpkin tossing minigame. That took me forever until I realized that I had to cover the camera on the WiiMote. I'd like to see that be fixed. The other thing is kind of what Ian was talking about. Some enemies (and bosses) would require a swing in a particular direction, but you kind of had to put your hand in position to swing the sword that way. Doing so too quickly would register a swing in essentially the opposite direction. That took a bit of getting used to. That being said, I could take it or leave it. I'd rather see what Nintendo could do with the uPad.
Either way, I don't wanna see another touchscreen Zelda. I didn't finish Spirit Tracks because I got sick of the controls.