Imagine walking through a dungeon via the analog peripheral. A stalfos jumps out at you. You point the controller at the screen, click on him, thus A-targeting him, and begin swinging your arm through the air wildly, effectively slashing him to death on screen.
-OR-
Maybe it's not so physically intense. Maybe you walk into the dungeon using the controller's gyroscopic technology and when the stalfos leaps at you, you point at him, hit the button on the back (a la Z-targeting), you now have him B-targeted and you can begin hitting the A-button rapidly, slashing him to death.
-OR-
It could be a combination of the two. Where you walk into the dungeon using the analog stick, point at the Stalfos, B-target him, and slash away with the A-button. That sounds best to me. In fact - that seems like some of the most fluid gameplay I've ever heard of.
I believe that Nintendo may have actually found something here. It's bold and crazy and insane - but since when has Nintendo ever gone the straight and narrow? You're talking about the company who introduced a platformer where you use Bongo drums to move around. But you're also talking about the company who kicked off the video-game market as we know it today and introduced the rumble feature to video games and vastly improved wirelessly controlled gaming so much so that it is now the standard. They aren't completely stupid.
Besides - there's still the casing you can put the controller in that's supposed to look like a wavebird - so even if you hate the controller, you can at least swich it around a little bit.