To clarify, obviously all elements are all stories are there in the black and white but what I'm really referring to is that in most stories, there are components that the reader is actively aware of, the surface of the story: the general plot line, the sense of the characters and hopefully the setting as well.
I find that a truly great story has layers underneath, aspects of the development of the plot and the character and the physical style and structure that is not readily noticeable to the reader. The pacing that pulls the reader through at various speeds as desired, the thread of the various plot lines that lend drama and style. They are all aspects of a really great story that I, as a read, am experiencing as much as reading.
Those elements of story-telling are the 90% of the iceberg.