While some battles might be more pitched than others, Yu-Gi-Oh protagonists typically win their duels. Whether it be with the aid of an Ancient Egyptian artifact, dragons that at one point helped to seal away evil forces beneath the surface, or even duel spirits, these protagonists help restore a sense of normalcy to their respective worlds when they're put in danger. Across the franchise's various installments, Yugi Moto is perhaps the most popular protagonist, as he led the original series. However, Yugi is far from the best duelist protagonist in the franchise.
Despite his prowess, Yugi wasn't undefeated, and several of his duels featured questionable moments. For example, Yugi lost his first battle to Pegasus in a sort of Shadow Game, failing to defeat the villain within the time limit provided due to the limitation of his cards. Still, losing this duel is what actually forced Yugi to travel to Duelist Kingdom and kickstart his dueling career in the professional circuit.
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Another well-known loss occurred when the Pharaoh took on Rafael during the "Seal of Orichalcos" arc. Headed by the villainous Dartz, the evil organization Doma collected souls for the purposes of waking up the Great Leviathan and bringing an end to life as the characters knew it. Over the course of this arc, Yugi and his friends had a lot of struggles. It started with Yugi losing the Egyptian God Cards to the group, despite the fact that he won the duel where these cards were waged. Mai Valentine then switched sides and joined the villains. With all of that going on, The Pharaoh dueled Rafael and lost, causing Yugi's soul to be put in danger.
This duel itself represented a low-point for the protagonist of the original Yu-Gi-Oh series. Normally, Yugi and the Pharaoh served to complement each other. However, with Yugi out of the picture, the Pharaoh felt as if he was alone inside. Of course, Yugi's other friends supported the Pharaoh and ultimately helped save the hero, but he went through his own period of grief. This showed that not even the "King Of Games" was the perfect duelist.
Most Yu-Gi-Oh franchise protagonists have losses of one type or another. Examples include Jaden's loss to Aster Phoenix in Yu-Gi-Oh GX, Yuma's multitude of losses in Yu-Gi-Oh Zexal, Yuya's very first duel in Yu-Gi-Oh Arc-V and Yuga's loss to Rook in the ongoing Yu-Gi-Oh Sevens.
Surprisingly, Yu-Gi-Oh Vrains and Yu-Gi-Oh 5D both featured a protagonist who never really lost. While technically speaking Yusaku Fujiki/Playmaker lost in flashbacks set in his childhood, those duels occurred mostly off-screen and didn't hold the same weight as the series' key battles. 5D's Yusei Fudo, for his part, only really lost to Jack Atlas, which was also in a flashback. If the best duelist among the Yu-Gi-Oh protagonists was determined by who experienced the fewest losses, Playmaker and Yusei would be the two number one contenders for the crown.
However, what he has in wins he lacks in overall duels. Playmaker didn't duel nearly as often as other leading figures in the Yu-Gi-Oh franchise, with his series instead giving a lot more time for other side characters to shine. Admittedly, with their track records, Yusei and Playmaker could probably have beaten anyone. However, Jaden Yuki battled the most of any Yu-Gi-Oh protagonists by far, wracking up more wins overall than even those who went virtually undefeated.
Overall, either Playmaker, Yusei or Yuki is the Yu-Gi-Oh franchise's top duelist protagonist, though just who is actually the best is more a matter whether percentage of wins or volume of battles is given more weight. Regardless, a great duelist isn't necessarily the same thing as a great protagonist, and one's favorite hero is, at the end of the day, a matter of preference.