The Custom Duel theme gives a more serious remix of the tournament theme from the previous game. Bit of a waste since you'll never hear it anywhere other than the two-player mode against the various deck masters.
Badass Decay: This game saw the debut of the Immortal cards, which serve as a set of Infinity Plus One Swords. They had powerful effects, even aside from the natural benefits of being Immortal (immune to Crush terrain, and create it upon death, likely killing any opponent who beats them). Unfortunately, when they were released in the actual game, they mostly lost their awesome effects or were just plain not very good - only Slate Warrior and maybe Rigorous Reaver were still sorta playable. How bad was it? One of the Immortals was Shapesnatch. Yes, that Shapesnatch.
Critical Dissonance: The game got mixed reviews, but it still became a Greatest Hits title with over a million copies sold.
Critic-Proof: Likely the reason for the above. It was one of the first Yu-Gi-Oh! video games for home consoles released in the early 2000s at the height of the franchise's popularity — it was going to sell no matter what critics said.
Designated Villain: The Yorks are supposed to be the bad guys, but if you play both campaigns, it's pretty clear who's offering the better deal. If you side with the Lancasters, Henry VII gets crowned King and takes the credit for winning the war, to the point where you, who did all the work, aren't even mentioned in any recorded history, and it's unclear if you even returned to your own time. Meanwhile, siding with the Yorks leads to Seto treating you as an equal, even planning to share the the Guardian's blessing with you. When the summoning doesn't work out, he gives you a pendant that guarantees his family's debt to you, and gladly returns you to your own time. Furthermore, we're told that the Yorks have the Lancasters pushed into a corner, but a quick look at the actual map shows the Lancasters being everywhere and equally strong as, if not stronger than, the Yorks. On top of that, regardless of what side you choose, Henry becomes king anyway and Seto steps aside.
Game Breaker: A whole lot, the worst of them being very difficult to obtain, but the biggest one has to be Darkness Approaches. It flips everything on the field face-down, meaning flip effects can be recycled. A good number of cards power up themselves when they're flipped face-up, such as Wood Remains and Mystical Elf. Not only that, Fiend Reflection #2 lets you play another card the turn it's flipped, and even worse, Magician of Faith and Mask of Darkness can recycle spell cards. Including Darkness Approaches, which then flips them face-down, creating an endless cycle. Admittedly this is a card you need to be very lucky to obtain.
The easiest one to obtain and work with are Zombies. The person using them is fightable as the second opponent in one campaign, and despite his low deck cost he isn't extremely difficult to beat. The archetype runs on two principles: Multiple copies of Dragon Zombie, Armored Zombie, and Clown Zombie, three monsters with extremely low cost for their attack power and low Level (They exchange this for Defense, which you rarely need), and the ability to summon multiple copies of Pumpking The King Of Ghosts (through normally summoning him or through fusing a Zombie and a Plant together, when one of them is at or above 1000 attack). Pumpking by ITSELF is a Game Breaker, as its ability (Raise the Attack and Defense points of all Zombies permanently by 100 every player turn) allows for insane ramping of power even with only one on the field. Throw in Wasteland to set the terrain, a few more cheap Zombies, and just a few more cheap cards (like Swordsman From A Foreign Land and Cursebreaker) into the deck and you have an easily obtained deck that can beat 90% of the game without modification. Add in call of the Haunted and/or blue eyes silver zombie, to change all your non zombie monsters into zombies to get pumped. Just watch out for crush terrain. Or use a field spell to remove it.
Perfectly Ultimate Great Moth is pretty nasty. It has the ability to lower your opponent's attack and defense on every creature (even face down) permanently every turn as long as it stays in face up defense mode. A few duels with Weevil can get you the cocoon of evolution and a Petite or Larvae moth to fuse with it to create Pupae of Moth, which turns into perfectly ultimate great moth next turn, and goes to the graveyard. Where it can then be resurrected with a card to get you another moth (Mimicat is commonly used for this). Then it goes to the gravevard again. You can use these cards in your already gamebreaker zombie deck. Humiliation doesn't even begin to cover it.
Once you draw Mirror Wall (obtainable with a password at start of the game if you know it), you've practically won the duel. It's an incredibly powerful continuous trap that blocks all of your opponent's attacks and cuts their monsters' attack in half. However, due to Artificial Stupidity, the AI will simply keep attacking as if the trap didn't exist, weakening their monsters and allowing you to do whatever you like unimpeded.