Check out this interview with Charlie Kaufman, which includes this rare explanation of his intentions regarding Adaptation:
People are very critical of Adaptation’s ending, they think of the end as a failure. But one thing I’ve never seen in print is that that movie was intended to be a failure. Then, rather than make it about failure, which is a safe way to do it, I wanted the film to be a failure. That’s what happens; it’s about panicking and compromising, among other things. But when you’re watching the story play out, the writing of the screenplay, which is what you’re watching, it ends with an enormous compromise, and it’s a disaster, literally and figuratively. The character in that movie is the script, that’s the character you’re following, not the people. And I guess people can’t feel an emotional connection to a screenplay. But I thought it reflected a corruption of the man who was writing it.