The following characters are listed in the game's code: Harrington Rosewood, Damon, Belowski, Reginald Van Howell III, Missy, Sartorius Kumar, Lorenzo, Rose, Vice Chancellor Bonaparte, North Academy Chancellor, Laboratory Chief, Kumazo Huffington, Wheeler, North Academy Czar, Slade Princeton, Jagger Princeton, The Gambler, Mad Dog, X, Gerard, Gravekeeper's Chief, Yasmin.
Lines for Dark Magician Girl as a duel opponent during multiple points of the storyline.
Unused lines for Sadie and Dorothy, including an alternate version of the event in the game's introduction in which the player and Jaden help Dorothy with her truck.
Overworld icons for Sadie, Dorothy, Chancellor Sheppard, Nightshroud, Camula, Abidos the Third, Don Zaloog, Jinzo, Kaibaman, Dark Magician Girl, and all versions of Kagemaru, Blair, Zane Truesdale and Lyman Banner.
Unused Deck names with no associated Deck data: "Lone Hero", "Cyber Style", "Sheppard Chaos Style", "I'm the Heroine", "Hysteric Time", "Cutie Magic", "End of the World", "Birth of Evil", "Ruler of the Doomed", "Draw & Join", "Stairway to the End", "Forbidden Ritual", "Superior Machine Squad", and "Nightmare Guide".
Crystal Seer has an unused line: "Never lose to the courts!". This line seems to have been intended to be used as advice if the player visited Crystal Seer during the courthouse event in the World of Order.
There are lines for an unused NPC based on Green Baboon, Defender of the Forest.
There are sprites for Sasuke Samurai 3, Neo-Spacian Air Hummingbird, Magical Merchant, Elemental Hero Wildheart, Elemental Hero Stratos, UFOroid, Botanical Lion, Blue-Eyes Toon Dragon, Shinato, King of a Higher Plane, and Cold Enchanter as duel opponents. Most of them appear as opponents in World Championship 2007.
This Deck is not used in-game. It seems to have been used at Jump Festa.
There are bust-up sprites for Alexis and the Admiral based on their sprites from Spirit Caller, bust-up sprites for the Facility Chief based on his sprites from Wheelie Breakers, and crude blue bust-up sprites mentioning Leo, Luna and Tetsu Trudge.
Various Decks in Story Mode and in World Championship Mode include Side Decks, despite them being impossible to use. Reported by GameFAQs user deufeufeu
This Deck is not used in-game. It seems to have been used at Jump Festa.
The files used for Leo's and Luna's sprites are named Syanron and Kouryu, respectively. Other files for them use names closer to their Japanese names.
All voice clips and images from the Japanese release of the game are still in the game's files in the localization, including images from Jump Festa.
World Championship 2010
There are bust-up sprites for Seria as a duel opponent wearing her Arcadia Movement uniform, and dummy sprites saying "Dark Greiger" (ダークボマー, Dark Bommer) on the side.
This Deck is not used in-game. It seems to have been used at Jump Festa.
Syd, Ida and Kameno have in-duel sprites that face from the left to the right, which would only be used in Tag Duels if they were partnered with the player.
This Deck is not used in-game. It seems to have been used at Jump Festa.
There are various voice clips for Sherry LeBlanc as a member of Yliaster, including voice clips for "Necro Fleur", "Sorciere de Fleur", "Ecole de Zone", "Soul Binding Gate", "Z-ONE", "Imitation", "Fleur de Vertiges" and "High Half".
Saikyo Card Battle
Light Tsukiko has lines dedicated to "Magical Android", despite her not having that card in any of her Decks.
The game has largely-complete listings of card names in non-Japanese languages for all 729 cards in the game. The only localized names missing are for cards 6154, 11673, 12191, 12227, 12230, 12232 and 12570.
