According to game's planner/scenario writer Hiroyuki Takahashi & assistant producer from Nintendo Toshiharu Izuno in a 2001 Nintendo Dream magazine interview, when Hiroyuki read the scenario, he came to believe that if they included the full story then the full playtime would likely be over 100 hours. Hiroyuki had doubts about whether such an epic amount was appropriate for a handheld game, and thought 40 or 50 hours would be a better volume for one game.

Izuno added that there was no need for a fixation on having it all in one game, and that his team had the idea early in development to switch protagonists for the second half of the story. They planned for Jasmine, Garcia, and Sheba to be the leads in the second Golden Sun game, with Alex's fate left unstated until the game's release.