The first time I saw Adaptation, I thought the ending was horrible. And considering how brilliantly written the rest of the movie was, I couldn't get why it had this clunky ending that made almost no sense. Then someone pointed out to me that the movie is ultimately about failure. But since the main character is writing the movie we're watching, he couldn't succeed in writing a good movie. Which means the movie HAD to have a poorly written ending. Now that I get the point, it's one of the most awesome endings ever.
That or it was written by his brother. Hint: Watch what happens to the plot after he dies.
Except he doesn't actually have a brother. Charlie and Donald are both really him. Although I'm not sure how you would film that.
Actually, if you pay attention, the ending of the film is foreshadowed in the scene where Charlie pitches the film to his agent, where he outlines exactly what ends up happening. That means Charlie gave up on doing a true adaptation and ended up making the Hollywood version, compromising his moral high ground from the beginning of the film. Notably, this starts to happen after the writing instructor tells him to do it.
The movie's drastic tonal shift happens after Charlie asks Donald for advice on his script, leading me to believe that the last act of the film is to be interpreted as having been "written" by Charlie's overzealous brother. Remember how Donald's script seems to be the most cliche-ridden, mainstream Hollywood thing imaginable? That's exactly what the film becomes after Charlie asks for Donald's help in writing his script. The fact that Donald doesn't exist in real life is irrelevant.
As noted below, the movie becomes a thriller when Donald becomes co-screenwriter
In the beginning, when talking to the producer, Charlie mentions everything he doesn't want in the film: drug trafficking, sex scenes, shootouts, car chases, etc. Guess what happens in the last 30 minutes
In a similar tact, when Charlie sees Robert McKee's talk, McKee rants about the laziness of voiceovers (which are used extensively throughout the film) and Deus ex Machina
Charlie describes in his tape recorder several scenes we actually see (like the opening monologue, the birth of the universe scene, and the introduction of La Roche).
Donald's script The 3 is about a man with multiple personality disorder where the man is a killer, his own hostage, and a cop chasing himself. Charlie is holding himself hostage with his insecurities and Donald is an aspect of his own personality seeking to "free" him from these neuroses.
Donald thinks that the same actor should play all three roles, and when Charlie asks how, Donald mentions "trick photography". Charlie finds this incredibly stupid. Both Charlie and Donald are played Nicolas Cage.
Another example, particularly visible if you watch this movie in a double feature with Being John Malkovich. Donald notes that for The 3, he's decided upon a running theme of broken mirrors to highlight the protagonist's fractured psyche. Being John Malkovich notably features more than a few broken mirrors as John Cusack's character became increasingly disconnected with reality.