These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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. 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.
Even Better Sequel: The other side of the players loves this game because you spend much more time to play through, having an interesting story and this game allows you to play all three Egyptian Gods unlike the previous game.
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.
Another example: Why does Weevil show a hidden heart of gold and act somewhat nicer to the player? Because the player isn't Yugi/Yami Yugi. Therefore, Weevil holds no grudge against the player for anything like Duelist Kingdom and does not even lose to him in a tournament, averting a great deal of humiliation. Plus, unlike the Pharaoh, the player does not (apparently) laugh at Weevil. Thus, we see his nicer side.
Game Breaker: 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.
Marik. Justified as he's protecting the power of Ra, though. Making this worse is he's a required boss.
Mako Tsunami is up there, too, especially in the rematch.
God help you if Weevil Underwood summons the Perfectly Ultimate Great Moth. The guy is tricky enough with his traps and effect monsters as is, but if he summonsthatjuggernaut...
Every duelist in the game can qualify as this considering the horrible cards you start the game with, the low amounts of Deck Capacity you will be getting, and the ability for the computer to topdeck their best cards.
Sol Chevalsky can take out your Egyptian God Cards with his Red Archery Girl's effect, which lowers their attack and defense points and immobilizes your cards. He can also use Relinquished and Thousand-Eyes Restrict to steal your non-Egyptian God monsters, with Thousand-Eyes Restrict increasing their stats by 1000 points. He also has 20,000 LP and a Toon Summoned Skull, which only needs one tribute and it gains a field power bonus.
Reshef. 40,000 LP, all three God Cards (despite the fact that YOU have all of them), regenerating LP cards, enough traps and spells to inhibit your attacks, and he comes immediately after another battle. You can have a hard time beating him using ACTION REPLAY.
Odion is somewhere on this spectrum as well, although you can skip him and go straight for Marik instead. At the very least, he's a Wake-Up Call Boss, and you had better be prepared if you're confident/foolish enough to try to beat him and Marik back-to-back.
Arkana. With non-tribute monsters beefed up to over 1800 Attack with the Yami field and varied types of monsters, your only prayer for survival is to change the field type or get lucky with Final Destiny. Even then, it's an uphill battle.