- Actor Allusion: In contrast to his performance in GX, Takehito Koyasu is clearly channeling Dio in his voice work for Saiou/Sartorius this time around.
- I Knew It!: Many players predicted a GX world would be added down the line, as well as a 5Ds world.
- Name's the Same: The Dawn of Destiny mini-box shares its name with The Dawn of Destiny Yu-Gi-Oh Xbox game.
- The Original Darrin:
- Sam Riegel returns as Rex, having been replaced by Sebastian Arcelus in season 4.
- Tara Sands returns as the voice of Mokuba, here in the game, as well as in the Dark Side of Dimensions movie, having been replaced by Carrie Keranen in Season 5.
- The Other Darrin:
- While most of the original English VAs returned, Mako is now voiced by Daniel J. Edwards, sharing a voice with Aigami. Edwards also takes over the voice of Sartorius from the late Maddie Blaustein.
- Weevil is now voiced by Billy Bob Thompson and not Jimmy Zoppi, possibly due to the latter being busy with Pokemon, although Billy Bob does a near-indistinguishable job of replicating his voice.
- Jimmy Zoppi is also replaced by Wolfe Scott as Lumis.
- Para has his voice actor from episode 19, Sam Riegel, while Dox is now voiced by Eric Stuart as in Yu-Gi-Oh! GX.
- Espa Roba went from Sebastian Arcelus to Bryan Tyler.
- Yubel went from Cassandra Lee, her VA in GX, and Eileen Stevens, her replacement in the Bonds Beyond Time movie, to Alyson Leigh Rosenfield.
- The Wiki Rule: The Yu-Gi-Oh! Wiki, and the forked site, Yugipedia.
Trivia / Yu-Gi-Oh! Duel Links