Kaiba only showed Virus Cannon in his duel with Ishizu, and Cloning and Final Attack Orders against Yugi. It seems that both Yugi and Kaiba changed their decks significantly after their first duels in the Battle City Finals, judging by the fact that Yugi's duel against Bakura was the first time he even played Osiris (and by the time he fought Kaiba, he'd thought up ways to quickly gather Tributes like the King/Queen/Jack knights). Kaiba also never displayed use of the XYZ magnet monsters against Ishizu, as his deck in that duel was seemingly focused on forcing the opponent to Deck Out using Crush Card and Virus Cannon rather than decimating them with powerful monsters like the Blue Eyes variations and XYZ. (Albeit, he had Soul Exchange as a quick trump card to summon Obelisk.) Furthermore, Kaiba openly stated that he added Fiend's Sanctuary to his deck as a counter to Marik's Ra, which he didn't have intel on until after Mokuba took a satellite photo of it after Marik's duel against Mai.