There are a few instances in which Motion Controls worked better than a standard button format (Metroid Prime 3 springs to mind as the first example), but the problem is that a fair bit of work needs to be done in order to get motion controls to work effectively. While it sounds simple enough (point at the screen and the thing moves), due to all motion control formats lacking buttons, certain functions that would have to have been programmed to buttons now have to be assigned to motion control functions, and doing that intuitively and in a non-gimmicky way is difficult.
There's also the fact that motion controls, despite how far they've come, just are flat out not as reliable as a standard controller scheme (unless the motion controls involve pointing at the sensor bar and nothing else). People reference Skyward Sword, which is arguably one of the best example of motion control working. But that's the thing, even in one of the best examples of motion control working, I would argue that Skyward Sword's sword swinging mechanic will still give you an incorrect input about once every 20 or so tries; a 95% success rate. And this is one of the best instances of motion controlling in a game.
Buttons (unless they break) work 100% of the time. There's a drop in reliability, it's difficult to build a control scheme around it, and if you're developing a game for the other two consoles, which don't have Wii remote style controls (or, at least, didn't until the PS Move), it's hard to port a well done version of that over to a completely new control scheme. With the Wii's generally poor sales for third party titles, the sales factor could be enough by itself to convince people to not try anything new in terms of motion control.
