The character development. If the author can take Jaden Yuki's known traits from the original series and expand on them in a new and exciting way within the fanfic, it can be really interesting. For example, showing a more vulnerable or passionate side of him.
Romance is also quite prevalent. It could be a love story between female Jaden and another character from the series, like Syrus or Chazz. The authors often put their own spin on how the relationship develops.
One common antagonist could be the Society of Light. In fanfiction, they might target Jaden more aggressively than in the original series. They could try to manipulate him or harm him to further their own goals of 'purifying' the Duel Academy. Another antagonist could be a rogue duelist who has a vendetta against Jaden for his success. This duelist might use underhanded tactics to try and hurt Jaden during duels, not just aiming to win but also to cause him physical or emotional pain.
One popular theme could be Jaden facing emotional hurt from the loss of a duel. In many fanfictions, his confidence takes a hit when he loses to a powerful opponent. This can lead to him doubting his skills and going through an internal struggle to regain his mojo. Another theme might be him getting hurt physically during a dangerous adventure in the spirit world. He could be injured while trying to protect his friends or while exploring uncharted areas. And sometimes, the hurt can be more psychological, like when he feels betrayed by someone he trusted within the Duel Academy.
A common theme is friendship turning into love. The OC and Jaden start off as friends, maybe sharing a love for dueling, and then their relationship deepens over time. Another theme is the OC helping Jaden through tough times, like when he faces difficult opponents or personal challenges at Duel Academy.
First, know the character of Jaden Yuki well. Read up on his backstory, his mannerisms, and his relationships in the original series. This will help you create a more believable interaction with the reader. For the 'lemon' part, if you choose to include it, be subtle and build up to it. Don't just jump into it right away. Use descriptive language to set the mood and the emotions between Jaden and the reader.
One exciting plot could be Jaden facing a new and powerful opponent who uses a never - seen - before deck. This would test his skills and force him to come up with new strategies. Another plot might involve Jaden traveling to a different dimension where the rules of Duel Monsters are slightly different, adding an extra layer of challenge.
Well, another option could be to check out some dedicated Yu - Gi - Oh! fan forums. There might be threads where fans share their own Jaden Yuki lemon fanfics or recommend some good ones they've read. But be aware that the quality can vary greatly, so you might have to sift through a bit to find the really great ones.
The popularity might also stem from the fact that it offers a different perspective on the Jaden Yuki character. In the original series, his relationships are more platonic. But in these fanfictions, it delves into a romantic realm. The 'x reader' format makes it very inclusive for fans. They can put themselves in the story and experience a relationship with Jaden in a fictional but exciting way. The 'lemon' part, while it can be a bit more risqué, is also a draw for some fans who like that added touch of spice in their fictional relationships.
One great place to find Jaden Yuki x OC fanfiction is Archive of Our Own (AO3). There are many talented writers who create interesting stories in this genre. Some might focus on their adventures in the Duel Academy, while others could explore a more romantic side of their relationship.