Given his birthday yesterday, I feel like I should elaborate why Jaden/Judai (even though the two tend to be vastly different characters on occasion) is my favorite Yugioh protagonist.
An upbeat and challenge-loving shonen hero who's as capable of being an immature dunce as he is capable of showing emotion when run through the wringer is the perfect protagonist for this type of show, and his character development is still very unique for the franchise.
This is the reason why I was excited to see what direction were taking Yuya in Arc-V, which was sadly half-assed beyond belief by comparison. Jaden is still the only Yugioh MC you could tangibly feel become a different person by the end of his show than he was at the start.
He's periodically accused of getting fellated by the plot which really isn't much more of a case for him than it is for most of the other protags. The only time the story was explicitly a result of his actions (Season 3) lead to monumental changes to the show and him as a person.
The characters surrounding him are varied in such a way that his personality tends to bounce off perfectly from theirs, leading to very fun interactions with what I consider the best overall side cast in YGO. Not everyone in there loves him, but he earns their respect.
His design is also undeniably unique for the series. Incredibly down-to-earth compared to the rest of the series, but still striking and recognizably "Yu-Gi-Oh". Not to mention, his Season 4 redesign that did a phenomenal job at reflecting his growth and change as a character.
His Hero deck is still a charming reflection of himself as a person, not just aesthetic-wise, but in-universe as well. Small things like saying how his favorite card is Flame Wingman or seeing him build and fiddle around with packs brings a lot of personality into his dueling.