Story Layers

I recently read an excellent novella, "Act One" by Nancy Kress. (You can read the beginning in Asimov's Science Fiction). I believe it was a 2009 Nebula Nominee. The beauty of this story is it works on multiple layers.
One layer is the external plot: An aging actress named Jane Snow is researching her role in a controversial film about a recently discovered genetic modification. The real-life procedure is proliferated by a mysterious organization known as The Group whose long-term plans are to reshape humanity. Some see them as benefactors while others see them as biological terrorists. When Jane and her manager, Barry Tenler (the point-of-view character), meet with members of The Group they are the catalyst of a global conspiracy. Can Jane and Barry stop it? Deal with it? Survive it?

One layer is the fascinating issues of genetic engineering. The story raises the important and topical questions of the ethics of genetic modification. Should humans be genetically modified? When would it be all right? To save a life? To avert war? As you can imagine, there's a lot of thought-provoking content here.

One layer, perhaps the most important layer, is the character arc of the protagonist Barry. Barry is the perfect character to tell this story because he has to deal with his own genetic challenges. And, because of this challenge, he attempted genetic modification of his son. Suffice it to say, this didn't go well, and Barry's life totally fell apart. At the end of the story, through the events of the story, Barry learns to accept and deal with his personal demons and the effects his actions have had on the people who love him.
I believe it is this layer that elevates the story from good to outstanding.

As writers, we should always strive to show our characters changing, learning, growing as a result of the story. A nice (and free) example of this is "Heart of a Magpie" by Kathryn Yelinek in the current issue of Electric Spec. In this story the protagonist, Marion, has to deal with a supernatural menace, and she eventually utilizes the help of another supernatural creature to defeat it. What makes this story better than the average story is the internal layer, the character arc, of the protagonist. In the beginning, Marion is reeling from some unfortunate events, and blames some people in her life for them. By the end of the story, because of the story events, she comes to realize these people aren't irredeemable. She deals with her life in a more positive way, and starts on the road to forgiveness.
Now, that's what I'm talking about!

How about you? Have you read any good stories lately?
Do you have any tips for creating story layers?