He didn't flinch from geekdom. It wasn't prettied up, Hollywood geekdom in his movies, or at least, not all of it. Hughes's geekdom was awkward and painful. It was played for laughs, but they were always at least half-sympathetic laughs, which was rare at the time.
He didn't do issue films or bright, fluffy teen romances. He captured the pain of trivialities and the lack of perspective of teenagers. His parents weren't monsters, just caught up in their own lives. Still and all, I never watched a John Hughes film that didn't make me uncomfortable for all the wrong reasons.
Find out why at Quiche Moraine.