I think the biggest problem with motion controls is that everyone does it differently. The recognition system in place doesn't take this into account a lot of times. Some things are generic so they work for pretty much anyone (shaking to reload a weapon), but other things need extremely specific movements and some people can't get those done, or they spazz out under pressure. Heh, my roommate does that all the time, which is why I call him a button masher. Motion controls aren't good for spazzing, which is how a lot of people play.
If we used more controlled responses for games, then I think we'd see less "waggle", but that's just not the case. Personally, I haven't had any problems with motion controls and would love to see more people use them, but lots of people simply don't know how to play that way and it causes all of these "control" issues.