It is clear that John in the novel is an outsider in every sense of the word. Huxley uses the character of John to comment on the so-called "advances" that civilisation has made in his future dystopia. It is clear that in their desire to stop war and conflict, the makers of this world have done all they can to suppress freedom of choice and human emotion, and this is something that John protests against, ultimately exercising his free will in his choice to commit suicide as a response to life in this "brave new world".
One aspect that John cannot understand is how death is treated. He is rebuked for crying at the death of his mother, in case the children who are visiting the hospital begin to realise that death isn't actually a fun event. His perfectly normal and human emotions of grief at the death of his mother have no place in this world.
Secondly, the promiscuous attachment to relationships is something that he cannot comprehend or understand. His outlook on life comes from Shakespeare, and so the promiscuity that is encouraged in this novel is something that disgusts him, and arguably is a factor that leads to his decision to commit suicide out of self-disgust after the orgy he has been involved in.
Lastly, the world of this novel is rigidly stratified, with 5 genetically engineered classes. The top class, the Alphas, are physically attractive and light skinned. The bottom class, the Epsilons, are dark skinned and ugly. However, because John has not been conditioned to accept this social system, when he sees a dark-skinned person from this group, he associates him with Othello, who was both dark-skinned and noble. He is able to see people for who they are rather than being blinded by social class.
Therefore the character of John in this novel is used to expose the weaknesses and failings of this future dystopia in robbing people of emotions and freedom of choice. To live in this world, it is therefore suggested, is not to really "live" at all.