I am arriving very late to this. I have just read a book of short stories by Neil Gaiman whose work I really like, and I found a little gem of a short story. It is called Goliath and it is set in the Matrix universe.
I admit that I have not read a lot of science fiction at all, but I truly enjoyed this story, which describes the Matrix in a way that I find much more compelling than that movies.

Gaiman wrote it upon request from Warner Bros, it was posted on the Matrix official web site before the first movie was even released, together with a few other stories from other writers.
The web site has been since removed, but the story has been published as part of a collection and, apparently, it has been published as a graphic novel as well.

It is a very short story, but in those few pages, Gaiman was able to fully take advantage of the possibilities offered by the idea of a world based on the Matrix concept. No much logical explanation is provided, we understand what is going on as the main character does. Gaiman, as usual, introduces a couple of twists. The main character has many physical flaws in his life in the Matrix and he is surprised to find out that he does not in the real life, detached from the machines.
Also, there is a switch in the story of David and Goliath.
It is smart and also moving.  I was ambivalent about the movie story line and now I wish that they had used this story for it.

The collection is Fragile Things: Short Fictions and Wonders.