There are many different kinds of movies. This is one of a rare species: a film with a message. Other people might hear different morals when watching it, or none at all, which is okay, too. But to me, Charlie Kaufman wants to tell us "deprive an adolescent of his right to a natural sexual development and you create a violent outburst".
Director Michel Gondry presents you a satire. The comedic element comes from grotesque, which is a relief after the all too juvenile teen movies that pathetically try to generate laughter by gross embarrassment and over-emphasized sounds of rearward body functions.
Instead of telling the story of average parents struggling to deal with their teenage son, you will find a) a woman with excessive body hair (in my view representing all your everyday discontent with your true self), and b) a man with an obsessive compulsion to demand perfect table manners (which of course stands for the misuse of parental power to force his unfounded views onto his "son")
The adolescent in this film being troubled by his sexual awakening is not the usual cool, hip, handsome high-school kid that all the real cool, hip,... okay-looking high-school-kids don't want to identify with anyway. It's Puff (Rhys Ifans), a young man who was raised by a deranged father to believe that he is an ape. This brings him in a situation not totally unlike that of a (human) teenager: somehow like the other humans, but being told that he's all weird and that everything he knows is suddenly wrong and bad. Eager to learn and please, he tries his best to conform, but to "control", that is, to ignore and deny his sexual curiosity, is just asking too much and he is forced to resort to deception.
It always amazes me how we Americans keep wondering why we have about 200x more shooting deaths than (other) civilized countries. One reason can be seen in the ratings for this particular film. Europe: around 12 (France: PG), USA: R, for it's hard to spot nudity. This is ironic confirmation of what the film is trying to draw attention to: by demonizing Puff's sexuality and using violence to suppress it, both Nathan and Lila become guilty of creating violence in turn.
For viewers who find this to be what this movie is about, I strongly recommend Michael Moore's Bowling for Columbine (Title 0310793 here on IMDB.com) only it is not so funny, because it's a documentary.
