Having read quite a bit about the education of gifted children over the past few years, something that struck me about John was that he concealed his intelligence in order to fit in. I remember reading that a child who does this can seem to 'have it all' - popularity and success - but they themselves know that the person who is popular is not them - it's a construct. They fear that if they were actually known for who they really are they would be disliked, but they've hidden who they are so successfully that no-one can ever get to know and like the real person!
On Atlantis the scientists - and Rodney in particular - validate John's intelligence, a key part of the real self he hides.
Another thought
On Atlantis the scientists - and Rodney in particular - validate John's intelligence, a key part of the real self he hides.