Everyone of the not-Elite Four final bosses of the GBC game are obsessed with playing their signature legendary cards who are clearly in the Awesome, but Impractical zone. The issue is that the energy cost for these cards are so crippling (6 energy cards attached to a single card, plus requiring a coin flip to do only decent damage?) and the AI prioritizes giving them energy over anything else, to the detriment of any useful cards in their deck.
The Computer Is a Cheating Bastard: Every single move in the games is planned out by the computer in advance, so reloading and trying a turn with a coin flip won't change anything. This also means the computer will deal out starting hands that will make the matching totally Unwinnable and there is nothing you can do about it.
Even Better Sequel: The second game is much longer and has more cards, allowing for more diverse strategies. It also has an actual plot, and the characters get a little bit more development. It's a shame that it never got an international release.
Fridge Brilliance: The Castle in the Game Centre in GR Island of the 2nd GBC game has duellists formed after Chess pieces. However, the Queen herself says that the castle has no King. The logic comes from the fact that, before the Queen, the player had already duelled a Pawn, a Knight, a Bishop, and a Rook in that order... more specifically, the order of the relative strength the actual chess pieces have. The King piece is around the strength of a Knight or Bishop, meaning that a King duelist would either be an Anti-Climax Boss or would have to be located between the Knight and Bishop (making a jarring inclusion).
Murray, leader of the Psychic Club in the first game. His deck is based around Stall, playing key monsters such as Chansey and Snorlax to soak up damage with their massive HP pools and using Scoop to return them to the bench with out losing energy. On their own they can just take attacks or attack, but Murray can also use Alakazam's Pokémon Power to transfer any damage he takes to any of his benched Pokémon (Like Chansey or Snorlax). Even worse, Murray can use Pokémon Center to heal all the damage you've manged to inflict on his active and benched Pokémon. Losing to him because of a Deck Out is very possible. On the other hand, if you load your deck with colorless types resistant to Psychic, beating him because of a Deck Out is also possible, since he loves using Kanghaskhan's "Fetch."
Hiderō/Bernard, leader of the GR Fire Fort, in the second game boy game. His "special rule" is easily one of the most unfair in the game: Fire type Pokémon have no weaknesses! Why is that so unfair? Well, unlike the other masters' rules, there's pretty much no way to possibly use this to your advantage, since his deck doesn't have any Water cards to hit your Fire types' weaknesses. So basically, it's just The Computer Is a Cheating Bastard disguised as a rules change. His deck is by no means bad either, and with no weaknesses to exploit the only real strategy is just to play really, really well. Or hope his A.I. Roulette gets handed the Idiot Ball.
Viewer Gender Confusion: Even though 'Murray' is a male name, his long hair and purple top gives him a feminine appearance.
Occasionally attack name translations differ from the main video game series' to better fit the context of the card game move's effects; for example, "Nenriki" (literally "willpower") is "Confusion" in the video games (it has a chance of confusing the opponent) and "Psyshock" in the card game (it can cause paralysis).
The Fan Translation of the sequel is one of the very rare examples to change character names, most likely so that the characters that debut in this game don't have names that stand out too much. Like in the main series but the unlike the first Trading Card Game, they are given Punny Names based on their specialty (so the Grass Fortress leader is Parker, the Water Fortress leader is Brooke, etc.)