Alternate Character Interpretation: Shadi and Ishizu claim Pegasus was unknowingly possessed by Reshef, but Pegasus himself says that he let Reshef into his heart. Which is correct is up to the player.
Anti-Climax Boss: Relatively speaking given the game's difficulty, Bandit Keith. A full third of his deck is made up of tribute monsters, and that rises to half his deck when you include his Spell cards that only work on one of his tribute monsters, thus it's very possible for him to end up with a dead hand full of monsters he can't summon. His non-tribute monsters are mostly Fiend-attribute save for the Fire-attribute Blast Sphere, so a couple of Light monsters can quash them easily. Or you can just use Umi to change the field to Ocean, giving his Machine monsters a 30% penalty to their stats. All in all he's not too much tougher than most of the Ghouls you faced before getting to him. And for the ultimate insult, if he manages to summon The Winged Dragon of Ra against you, laugh at him as you witness it's 0/0 stats since he doesn't know how to release its Battle Mode.
The Kaibaland plot, though it overlaps with a Heartwarming Moment as Serenity is super happy to see it.
The optional sidequest where everyone thinks Tristan/Honda has turned into a robot monkey.
Another optional moment where Téa gets hit on by Johnny Steps and the penguin-themed member of the Big Five. This is because of a fortune-teller saying she'd have bad luck with men.
Contested Sequel: Given that Sacred Cards was very easy, some consider Reshef's intense difficulty spike to be an improvement, others cite it as Fake Difficulty by way of The Computer Is a Cheating Bastard. The card pool is larger and the gameplay more complex than Sacred Cards, which allows for more intricate strategies while still capturing some Early Installment Weirdness, but the changes are also the source of the game's main Scrappy Mechanics and many of the more interesting cards are at a high-enough level that you probably won't get to use them for most of the game. The story, too, tends to drive a wedge through people, with some naming it Better Than Canon for taking advantage of the universe of the series and featuring some neat twists and turns, and others labeling it a bad fanfic that crowbars every character it can think of into the plot for no reason.
Escapist Character: Your character. He gets to hang out with Yugi and Joey, save the world, and even beat Kaiba in a duel! You own six of seven Millennium Items and all three Egyptian God Cards, and if you're lucky, even The Winged Dragon of Ra in Phoenix Mode. You're the coolest character in the world.
Evil Is Cool: Pegasus, who sports a ponytail and a golden eyepatch and stays one step ahead of everyone for a majority of the game.
The Winged Dragon of Ra's Phoenix Mode can be discarded in the hand to immediately appear on the field in Battle Mode, negating the need for three tributes. note It doesn't necessarily guarantee a win, though, if your opponent can lower its Attack/Defense Points with Effect Cards or Umi.
Dark Flare Knight can similarly be discarded from the hand to immediately summon Mirage Knight to the field, a 2800/2000 monster that normally needs two tributes. Mirage Knight then splits into a Dark Magician and a Flame Swordsman on the opponent's next turn, giving you two powerful beatsticks. Provided you can afford it in terms of money and deck capacity, there is no reason to not run Dark Flare Knight in most any deck you may end up building.
Castle of Dark Illusions constantly turns your monsters face-down, acting as a continuous version of Darkness Approaches. It also constantly turns the field into the Yami field which conveniently gives it a 30% power boost, creating a 3250 DEF wall with no drawback. However, its absurd deck cost makes it unlikely for a player to even run it until postgame, unless they somehow take control of an opponent's copy.
The Paradox boss rush has you winning cards from the Millennium Guardians you defeat as well as specific cards afterwards, meaning you can keep defeating the first Guardian to get a ton of Kuribohs to wager on duels, or keep beating the third Guardian to amass Giant Soldiers of Stone for large sums of money.
Hilarious in Hindsight: When Tristan is seemingly turned into a robot monkey again, Mokuba mentions that KaibaCorp had once manufactured robot monkeys that could duel, but they didn't sell well. Not long after this game's release, GX introduced a cybernetic monkey created by KaibaCorp that knew how to duel.
Besides all the computer cheating and loading issues, the game's Elemental Rock-Paper-Scissors system can easily be turned against you, like killing a Blue-Eyes with a Kuriboh.
You're forbidden from selling or anteing a card unless you have at least two copies of it in your card trunk. While this was ostensibly done to try and stop Unwinnable by Insanity scenarios where the player has no cards to ante and no money to buy more, in practice it'll often mean you win high-level cards you won't be able to use for a long while and may not even want to use anyway, and you have to let them sit in your trunk forever instead of being allowed to sell them to buy other cards or anteing them to win stronger cards.
Weevil, for one simple reason — Perfectly Ultimate Great Moth. A Divine-attribute monster with 3550 ATK, and his Forest field powers it up 30%. If he manages to keep Petit Moth or Cocoon or Evolution in play for only a turn or two, you'll find yourself facing one of the strongest monsters in the game fighting on its home turf. Good luck.
Arkana. He not only runs high-powered monsters, in the 1400+ range, with a variety of attributes, but he has the Yami field to give all of them 30% power bonuses and several power-up cards for them too, letting him quickly blast apart your Life Points with only a turn or two of leeway if you can't get an advantage on him.
Marik. He runs high-powered monsters in a variety of attributes, so it's pretty much impossible to stack your deck with opposing-attribute monsters like many other opponents. He'll use Newdoria, Widespread Ruin, and Raigeki to destroy your monsters, Viser Des and Spellbinding Circle to sap their power, Swords of Revealing Light to stop them from attacking, and then out comes Monster Reborn to revive them for his own usage. Oh, and he'll heal himself with Soul of the Pure.
Odion is an optional boss faced before Marik, but he's no slouch either. He runs a lot of Traps, so when you attack there's no telling what's coming, but odds are it's going to destroy whatever you attacked with or at least stop its attack. He also runs three Swords of Revealing Light, three Monster Reborn, several field-clearing cards like Heavy Storm, Raigeki, and Dark Hole, and finally he has several powerful tribute monsters, including the Divine-attribute Tri-Horned Dragon.
Shimon Muran. He runs monsters with upwards of 1600 points in most every attribute in the game, making it impossible to reliably counter him via Elemental Rock-Paper-Scissors. Further, he has several tribute monsters that are Divine-attribute, completely immune to that strategy anyway. And most surprisingly difficult is that Shimon only runs three Spell and Trap cards, unlike other duelists up to that point. This unfortunately means his deck is almost entirely composed of monster cards, hence he'll be able to summon those high-powered monsters every single turn with no let-up. If you manage to summon a good monster against him, you still aren't safe, because he has Reflect Bounder to deal damage to you equal to your monster's ATK. Finally, he's fought at the end of the Millennium Guardian Boss Rush, so you probably aren't in the best of shape in the first place.