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.

There are four unused items in the game's memory obtainable only through GameShark codes or debug rooms:

• Masamune: A Long Sword-class Artifact weapon, increases base attack by 115 and has no unleash effect. It has a unique graphic that is not seen legitimately in either this game or Lost Age.
• Sol Blade: A Long Sword-class Artifact weapon, increases base attack by 138 and has no unleash effect. Its 138 attack power is the highest out of any weapon in this game, surpassing even the 135 attack power of the Gaia Blade, this game's ultimate weapon.
• Kusanagi: A Light Blade-class Artifact weapon, increases base attack by 135 and has no unleash effect.
• Mysterious Robe: An Artifact robe, increases base defense by 40 and has no secondary effect.

Most of these items became proper, fully-coded items in the game's sequel, Golden Sun: The Lost Age

In the first Golden Sun game, you can get a "bad ending" near the beginning of the game. After the events that occur at Sol Sanctum, the Great Healer will ask you, "Will you accept responsibility for the fate of the land?" If you say no and leave the room, the screen will turn grey and display the text "And so the world began drifting toward its fated destruction..."