The villains of the Yu-Gi-Oh! anime all certainly range when it comes to quality. Some are great, some are strong, and others are Noah Kaiba. But, they can't all be knockouts.
Two of the most iconic villains in the show's history, however, are Pegasus and Marik. As the two original evils that Yugi had to face off against, they proved to be incredibly devious, each of them almost achieving their goals in the end. While they're both great, they each have their own strengths and weaknesses that make them very distinct from one another.
Pegasus: The Creator Of Duel Monsters
No duelist can't get much better of a villain than the creator of Duel Monsters to face off against. As the creator of the game, Pegasus had access to cards that other duelists couldn't even dream of.
It really rigs the game in his favor (among a few other tricks that he had up his sleeve). Facing off against the creator of the game that a duelist is playing isn't easy, making him quite the fierce opponent to take on.
Marik: Far Crueler
In general, Marik is a far crueler villain than Pegasus. Take his duel with Mai as an example. He was taking pleasure in his constant torture of her, and he did this with all of his major duels.
He had no qualms will killing, torturing, or anything else needed in order to achieve his goals. While Pegasus wasn't exactly a nice person, he certainly didn't ever reach the levels of widespread evil that Marik did.
Pegasus: Was Only Defeated By Yugi
Pegasus was a strong villain, very few were able to stand against him. Even Kaiba was taken down by him. The only person that was able to stand against Pegasus and win was Yugi, no one else stood a chance. Marik, on the other hand, was challenged by most other duelists he fought against.
None of Pegasus's duels provided him any challenge except for his last one against Yugi. The two were simply on two different levels.
Marik: Had To Work Against So Many Forces
One has to hand it to Marik, while Pegasus's only real threat was Yugi, Marik was dealing with far more opposition. Besides Yugi, Joey, Kaiba, Ishizu, and Mai all played their part in trying to take him down. He was in a far worse position than Pegasus, and still almost made it out to the other side.
If it weren't for Ishizu, Marik would have been unstoppable with all the god cards, so everyone really did their part in stopping him.
Pegasus: Had A Much More Human Side
Marik had a pure lust for power that drove him to attempt to take over the world by any means necessary. All that Pegasus wanted was to bring the love of his life back after she passed away.
While his means to get what he wanted weren't at all noble, he at least had a more human side than Marik. While Marik had an evil and a good side to him, both wanted the same thing. Pegasus didn't do the right thing, but it's understandable why he did what he did making him a better character and villain.
Marik: Controls The Rare Hunters
While Pegasus is mostly a one-man operation, Marik actually controls a whole group of evil-doers, the mark of an evil mastermind.
This allows Marik's evil to have a greater reach through many evil hands.
Pegasus: Is Actually A Good Duelist
To put it a bit more bluntly, Pegasus is a good duelist. He has great combos and knows what he's doing. Marik isn't necessarily a bad duelist, but if it weren't for The Winged Dragon of Ra, he would have been blown out of the first round of the Battle City finals by Mai.
He isn't on the level of Pegasus, but the creator's dueling skills don't come from fully above the board methods. Pegasus is a cheater.
Marik: Doesn't Cheat
Marik might not be the best duelist out there, sure, but he isn't a cheater. Pegasus uses cards that no one else has access to while also viewing his opponent's cards with his Millenium Eye.
No duelist could even hope to compete against that, they can't. They don't have the ability to cheat like Pegasus can so easily. Pegasus is a strong duelist, of course, but his cheating is what really seals the deal for him.
Pegasus: His Arc Leads To A Greater Good
Pegasus isn't seen all too often outside of season one of Yu-Gi-Oh!, but anytime he is, he is on the side of Yugi and friends. While he did horrible things during season one, he works to atone for his mistakes during season four, being one of the only ways that the gang was able to defeat Dartz.
He also helps out during The Pyramid of Light movie. He's never a main character again, but he is on the side of good after being defeated. This makes him an excellent villain because he experiences character growth.
Marik: Started From Childhood
Marik really embraced being evil from day one. Marik's evil side came out when he was a child, during which it ended up murdering Marik's father.
Pegasus was a lot of things, but he wasn't pure evil as a five-year-old. That distinction belongs solely to Marik. It isn't a great distinction to have, but it is Marik's and Marik's alone.