The point I'm arguing here is that the the Yu-Gi-Oh! Duel Monsters anime deviated from the manga for the deliberate purpose of appealing to Yugi X Kaiba shippers, whether because whoever was behind the anime thought it was more marketable or because they personally preferred it. I'm also running on the assumption that it's the latter.
The most obvious point is that the filler in the anime largely serves to make Kaiba more important, but that's excusable. Kaiba's the Vegeta of Yu-Gi-Oh! He's edgy without dipping into Liefeld territory, he's marketable, it makes sense to promote him. But I think that when you combine this with the other changes the anime makes, it becomes increasingly clear that they want to open up the possibility of Yugi X Kaiba hatesex.
First looking at Yugi himself. In the manga, Yugi and Joey trade porn and complain about it being pixelated. It's shown early on, but it comes up again. He also does a lot of blushing over Téa, and even Mai when he first sees them. So Yugi's a teenage boy and is attracted to women.
There's also this love triangle thing going on. Yugi is attracted to Téa, and tends to get flustered whenever other people are getting too close to her. Meanwhile, she's attracted to Yami Yugi, who doesn't seem to care one way or the other. Unfortunately for Yugi, she doesn't initially realize that they aren't the same person. Yugi's aware of this, so he tries to push Yami Yugi and Téa together. Honestly, I think it's a little underplayed in the manga itself, and the resolution's kind of weak. I would have liked if the anime built up on this, but that was not to be.
No, the route that the anime is to nuke all of that. There's no conversations between Yugi and Téa about their feelings anymore. She's completely out of the way. And now Yugi doesn't react to women at all. You might think that makes him asexual, but you have to use yaoi logic here. You have to work backwards from the assumption that Yugi and Kaiba are lovers. All those times in the manga that Yugi wasn't gay were just inconsistencies, the anime just cleared things up.
It does retain an event where Yugi sets Téa up on a date with Yami Yugi, but that didn't go anywhere anyway because Yami Yugi is brooding over his lack of memories.
So now we know that the people making the anime wanted Yugi to be gay. But that doesn't mean that they wanted him to be with Kaiba, right? He could be in love with any guy. That's true. So the anime goes a step further and sabotages the competition.
The first thing that needs to be clear about manga Joey is that he's the secondary hero of the series. He appears in all the arcs, half the volume covers (only less than Yugi himself), and a large number of the battles are his. Whereas Kaiba was originally intended to be a one-off villain and Duel Monsters was supposed to be a one-off game, Joey was a main character from the first chapter. Plus there's the thing where you can put the first part of their names together to get the Japanese words for friendship. I don't think the anime removes this stuff, though it buries it with a ridiculous amount of filler (about 40% of the series).
The other thing about manga Joey is that he is legitimately badass. He doesn't win everything like Yugi and he's still afraid of ghosts and the occult, but he's got a big winning streak for fist fights and similar "games".
In one case, Kaiba has set up a game of laser tag where Yugi and friends are playing against actual assassins Golgo 13. Also, the game is set up so that if Yugi or his friends are shot they die, while the assassins can just ignore getting shot. Tristan's the one to win this game, but Joey gets him a head start. As soon as it starts, he gets overexcited and ends up giving a green beret a flying kick to the face.
Did I mention how manga Kaiba was fine with cheating and killing at first? He also got his three Blues Eyes via extortion and his mob connections, and he pushed multiple people to commit suicide. Just thought I'd mention that. Anyway.
Another game has Joey in an enclosed room with tar covering the floor, fighting to the death with Leatherface. He wins. He also wins a fight against some Bruce Lee wannabe who sucks at Street Fighter, while holding a knife in his teeth blade-in. Plus he wins a yo-yo fight.
But Thammy, you say, this all happened before everything became focused on card games so it makes sense that they'd skip it. And that would be a fair claim. Yet the anime also goes out of its way to change other things to make Joey seem weaker.
The one that most threatens the Yugi X Kaiba relationship is Bandit Keith. In the manga, Yugi catches Bandit Keith after he sneaks into Joey's room to steal his tournament entry card. Bandt Keith decides to beat Yugi up so that he'll have to drop out of the tournament. This turns on Joey's friendship mode, so he wakes up from the deep sleep we just saw him in, totally overpowers Bandit Keith, and leaves him with a bloody nose. Joey notes that he's only stopping there because he wants to beat him at cards later too. As you can tell, this is just too powerful a piece of evidence in the hands of a Yugi X Joey fan, so the anime absolutely had to remove it.
The Kaiba fans behind the anime also had to make sure they proved that Kaiba was better than Joey, so they added a little physical altercation between the two of them before their match at Duelist Kingdom. Of course, Kaiba easily wins this, grabbing Joey's arm and throwing him to the ground.
Also, remember how in the Dungeon Dice Monsters arc, Joey spends the entire time in a dog costume being taunted by a cheer squad? Doesn't happen in the manga. He loses to Duke because Duke specializes in games that use trickery to give him an advantage, but Yugi figures it out and beats him so that Joey doesn't have to go through with anything embarrassing. The anime milks it just to shit on Joey more. Also Duke was trying to avenge his father, who Yugi's grandfather had magically aged into an evil clown. But that's neither here nor there.
Putting aside filler arcs, they also add another battle to Duelist Kingdom just for Joey to lose. He doesn't battle Yugi at the end of the tournament in the manga. He's already won the money and they'd just end up showing off their cards to Pegasus, so everyone agrees that the battle would be a dumb idea and Yugi should just go fight Pegasus right away.
So the anime turns Joey from a guy who regularly beats up people twice his size into a professional jobber. Since Yugi's an uke, he needs a real man like Kaiba to take the lead. By weakening Joey, they try to make him unable to perform that role.
For the last part of this argument, I think it's worth noting how Kaiba's changed from the manga to the anime. Manga Kaiba's still cool, don't get me wrong. There was a reason why he's popular. But remember what I said above about him cheating and killing people? Well, his character's a wee bit different, and it's definitely in that direction.
To start off with, the whole VR Duel Box arenas that he makes. When he first duels, Yami Yugi uses his magic to make the monsters actually appear on the table. Then when Kaiba loses, he punishes him by having him spend a day being hunted by images of monsters. Kaiba's scarred by the experience and ends up with recurring nightmares. So, naturally, he creates dueling arenas for the specific purpose of recreating this experiences, and then puts Yugi's grandfather through it to try to kill him.
His arrival on Duelist Kingdom was also pretty different. The henchmen on his helicopter have been paid by Pegasus to kill Kaiba. So when one pulls out a revolver to shoot him, Kaiba jams the gun's hammer by sticking a card in it, then breaks the guy's finger and takes the gun for himself. Then Kaiba makes both his henchmen jump into the ocean so he can fly the helicopter himself. And from there, he goes to Pegasus' castle, holds one of his henchmen at gunpoint to get him inside, then shoves his head in a suitcase and uses it as a footrest while he wave his gun around and demands Pegasus come to him.
And there's a whole arc consisting of games Kaiba's arranged to kill Yugi and his friends, but I don't think that needs to be said, right?
So anime Kaiba is a lot less evil than manga Kaiba. Part of it is probably to tone the series down for television, but I'd like to think that part of it is so that he isn't too evil for goody-two-shoes Yugi.
So in conclusion: the Yu-Gi-Oh! Duel Monsters anime makes Yugi less straight, makes Joey into a jobber, and makes Kaiba less off an antihero. This all serves to make Kaiba get into Yugi's pants.
