I hated it the first time I saw it in a movie other than the Matrix. In the Matrix, there is an actual reason people move like that, and the laws of the Matrix universe are clearly laid out in the movie, and the stop motion movements make sense when you understand the laws of that universe the movie creates. When it is used outside of that movie and used so often in other movies, it gets old real quick. I feel like the stunt choreographers in those movie, and the directors too, are lazy to come up with their own origianal moves, and have to steal from the Matrix without setting up an explanation in their own movie of how people can move like that. Heck, they even did it in the Lone Gunmen, a series I actually liked, but I just hated seeing it in there. It's not funny, it's not cute, and it's just plain annoying when people steal from other movies like that.
I only tolerated it in Shrek and Cats and Dogs, since those movies are actually good. But it does need to stop, but it will probably only get worse when Matrix 2 comes out.