Just read an entry about stinky movies over at dqg_neal's blog.
Whether it's on the screen or on the page, I believe the difference between a good story and a great one is the amount the protagonist (and possibly one or two other characters), changes during the course of the story. If you think about it, this even holds true for the great action movies, which you wouldn't think need such an emotional connection with the viewer/reader (think Die Hard, Bourne Identity etc.)
I've been trying to think of an exception that would disprove this theory. I haven't been able to come up with one.