I think the problem with motion controls is that they are not being used to define a new paradigm of interaction with the game(i.e. a set of movements and actions that are intrinsic to the gameplay and game mechanics). Instead, they are just being used to map same old standard button pushes to some arbitrary unique gesture(this is so each button push is uniquely identifiable). The movements are not designed as a continuous, choreographed flow from one set of postures and movements to another. Essentially, the motions need to matched with gameplay and game mechanics such to create a sort of smooth, precise dance, as opposed to an epileptic fit.
One could look at games like Dance Dance Revolution and argue that what I'm talking about is garbage because there was a dancing game with motion controls, but when you go through the motions, you like like a perplexed elephant stamping about with concrete blocks for feet. But, the problem with such games is they were still designed in the button-pushing paradigm and not designed with a more kinesthetic paradigm.
What I'm talking about would be a game where the progression of motion, postures, and gestures would look more like a smooth ballet or practicing of connected katas. The entire game would be an act of learning how to connect the motions and learning which motions, postures, and gestures naturally transition into each other such to create a singular, practiced flow of motion. Precision of angles, speed, and timing would all be important to the movements. Such a game could not only be entertaining but also provide great exercise, as well as improve dexterity and coordination. One could use such games to do things like actually learning how to dance, learning some martial arts, or, as mentioned, just engaging in some fun exercise(imagine a sci-fi space shooter with some rhythmically pumping trance or electronica that you have to actually dance to control, and I mean really dance, not the elephant-stomping DDR-style dancing).
So, in summary, motion controls generally suck because they are being used as simple mappings to traditional button-pushes rather than being used as the intrinsic new paradigm of control that they actually represent. One has to think outside the very small box of current traditional mainstream game design.