Yugi Muto is without a doubt the most celebrated duelist of all time in the Yu-Gi-Oh! anime. He's incredible and has very few opponents who have ever come close to defeating him. Yugi might be excellent, but that doesn't mean that he's perfect.
Yugi is pretty knowledgeable when it comes to deck building, but not every decision that he makes is in his best interest. A few tweaks would stand to make his deck even better than it already is. Maybe he wouldn't have even lost to Rafael with these changes?
Normal Ace Monster
Dark Magician is Yugi's most trusted monster, his ace. The one problem with this is that it's a normal monster. Despite being an absolute icon with a pretty solid stat line, Dark Magician doesn't have an effect of its own, which was a lot more prevalent when this card was released.
However, the remedy to this situation is that Dark Magician has plenty of support cards that target it and Dark Magician Girl.
Not Enough Dark Magician Support Cards
The problem with this, though, is that Yugi doesn't use a lot of these cards. Dark Magic Attack and Thousand Knives are two that come to mind right away, but there are plenty more that were around during this time.
He barely even uses Dark Magic Curtain in his decks. Yugi should really amp up his support cards for two of his most trusted monsters. It would certainly work out in his favor.
Not Enough Copies Of Dark Magician
It should also be noted that Yugi only has one copy of both Dark Magician cards in his deck. That just seems like an oversight. Additional copies would give Yugi more chances to use his two most powerful monsters.
In addition, Dark Magician Girl gets a bit of a power boost for each Dark Magician card that is in the graveyard, so more copies means more attack points for Dark Magician Girl. Everybody wins here.
Beaver Warrior
Yes, Yugi Muto really does use a card called Beaver Warrior, a low-attack normal monster that had absolutely no business ever being in his deck. He also used it during Duelist Kingdom, a time when tributes weren't even needed in order to summon strong monsters.
However, Beaver Warrior is not a single issue. It points to a bit of a larger issue, Yugi's Duelist Kingdom deck as a whole.
His Entire Duelist Kingdom Deck
While this can be said for basically every duelist during this arc, Yugi's Duelist Kingdom deck was not very good. It was filled to the brim with low-power normal monsters who brought absolutely nothing to the team.
The magic and trap cards weren't exactly well off, either. Overall, the power level would increase greatly following this arc, and Yugi wouldn't use many of these cards again.
Wildly Specific Cards
While this can really just be fully attributed to plot armor, Yugi's deck was full of cards that he would absolutely never use more than once, which is quite impractical when one really thinks about it.
Was Yugi ever going to use a card like Ragnarok in a normal duel that wasn't against a supervillain? No. That wouldn't make any sense. Mystical Refpanel? Probably not. Some of his decisions just don't add up.
Magician Of Black Chaos And Black Luster Soldier
Magician Of Black Chaos and Black Luster Soldier both have upgraded effect monster versions. As the two are ritual monsters, they're hard to bring out in general. Add in the fact that they don't have abilities, and Yugi shouldn't have been using these cards.
Dark Magician of Chaos and Black Luster Soldier - Envoy of the Beginning, however, are strong cards that Yugi should have implemented into his deck. Black Luster Solider - Envoy of the Beginning even still sees some competitive play in real life to this day.
Having Dark Sage At All (Sort Of)
Dark Sage is a waste of a space in a deck. It is wildly difficult to bring out and isn't nearly worth the effort. In addition, if it's drawn into, it is a dead card, as it can only be brought out when the effect of Time Wizard is used while Dark Magician is on the field.
Yugi shouldn't have had this in his deck given the truly rare circumstances which would allow it to be used.
All Sorts Of Normal Monsters
Whether it was Feral Imp, Curse of Dragon, Gaia The Fierce Knight, or any other one of the ensemble cast, it was very clear that Yugi used too many normal monsters in his deck.
Oftentimes, they also didn't have the statlines to back up not having an effect, either. They were just bad cards no matter what way the deck was cut.
No Spell/Trap Removal
Save for Mai Valentine, none of the main characters of Yu-Gi-Oh! had any good forms of spell and trap removal. Why that was will always be a mystery.
Cards such as Mystical Space Typhoon are some of the most important that you can have. Any duelist as skilled as Yugi should be able to see that. Instead, he chose to not include even one in his decks. This really would have helped him out.