A recent Famitsu interview has shed some light on the meaning of Bravely Default: Flying Fairy. According to scenario writer Naotaka Hayashi and producer Tomoya Asano, the title references the game’s overall concept, more or less meaning “Have courage and renounce the promises and responsibilities that are expected of you.” Basically, have the guts to do what you think is right. The Flying Fairy part of the title remains curiously unexplained.
The interview also revealed that Hayashi got involved somewhat indirectly. Assistant producer Shinji Takahashi recommended to Asano the anime Steins;Gate, for which Hayashi had written. As a result, Hayashi was tapped to develop the plot and character settings, with some of the more detailed work split up between Square Enix and developer Silicon Studio.