The other side of the argument is that you're fighting with the controls to try and find a relaxing position to immerse yourself in the game.  Sometimes motion controls work well, sometimes they don't.  But that's not the real problem in the long run:  

It's up to the player themselves to try and make the control scheme work well by creating as comfortable of an environment to play the game as possible: well positioned chair that allows for both good arm resting and elevation as well as the motion sensor in a good position.  Each gamer's exterior environment is something I don't think Nintendo ever considered to be a potential problem; not everybody has a way to make good room and most when playing long games don't want to stand up.  I always had to adjust my chair just right, or the motion sensor just right to get that perfect position.  Let's just say that people move things out of place often as well, either themselves or somebody else.  By accident or on purpose.  It can throw you off balance and make you not want to deal with the hassle. 

For some people having their arms elevated in a certain way to play the game properly and accurately for hours on end is also not comfortable.

It was done right in Skyward sword. And if the battles would have been more action oriented instead of puzzle oriented in that game, we wouldn't have this discussion.

Reggie makes some great points. Creating new puzzles and experiences is always welcome. The sword fights in Skyward Swords were badass like he states.

I never said remove them as an option. I said remove them from being the focus. Xbox still has the Kinect, Playstation still has the move. But Playstation and Xbox both focus on traditional controls

Nintendo has already went back to traditional controls as the focus.

In what universe is having a giant screen in the middle of your controller traditional? The shape, size, and feel change dramatically

Hardly, but more importantly is that the way you play games is the same. To make Link swing his sword, you press a button, not waggle a stick.

Not all games follow this. Some games force the use of the gimmick. Check out

edit: moreover, the controller still has a different feel to it. A lot of gamers switched to the Xbox 360 over the PS3 for this exact reason

I don't think one example is telling of their primary focus. Nintendo has completely given up on the Wii series, Zelda, 3D Mario, DK, etc. have ditched tacked on motion controls, and the majority of Wii U games only have motion controls as an option if at all.

But the controller itself still isn't designed to be traditional. It was designed to incorporate a giant touchpad. Like I said before, it changed the size, shape, and feel of the controller