Many cards that appeared in Yu-Gi-Oh! that were released in the TCG/OCG after their initial appearance are changed to reflect their real world counterparts. For example, "Negate Attack" is now a Trap Card with its TCG/OCG effect, rather than a Spell Card.
Gameplay was tweaked to be much more in line with the TCG/OCG. The only Spell Cards activated during the opponent's turn were Set Quick-Play Spell Cards in contrast to Yu-Gi-Oh!, where the activation of any Spell Card during an opponent's turn was commonplace.
Cards that debuted in GX but later became real cards sometimes had their effects toned down as in Yu-Gi-Oh!. After the release of the real card, the effect was sometimes changed to match its TCG/OCG counterpart, but not always. For example, "Future Fusion" used its anime effect until Season 3, when its appearance suddenly used its TCG/OCG effect. In contrast, cards such as "Elemental Hero Bubbleman" and "Skyscraper" used their anime effects throughout the series even after the cards were released in the TCG/OCG.
Replays are only applied in certain situations, and in others are ignored. "De-Fusion" causes attacks to lose their target, and replays generally do not occur when this happens. In other cases, such as the use of "A Hero Emerges", the number of monsters on the field changes, and the opponent opts to target a different one or cancel their attack altogether.