Plenty of franchises have had multiple protagonists throughout the years, but none have had the odd naming convention that Yu-Gi-Oh! protagonists have been given. All the protagonists have a first name beginning with "Yu," with the exception of Judai whose last name, Yuki, receives the convention.
Each of the "Yu" protagonists is unique, bringing something different to the table. However, some protagonists were better duelists or more compelling characters with better arcs than others. Additionally, some of the character's iconic cards were just as awesome in the actual trading card game, whereas others haven't contributed as much to the game that the show was created to advertise.
Yuga
Yuga was the protagonist of Sevens, an anime advertising a new game mode called "Rush Duels." Yuga's primary goal was to create a new and interesting mode of dueling that would separate him from the adults that play traditional styles of dueling.
As a duelist, Yuga is arguably the weakest of his entire main group of four characters. At the very least, he's certainly weaker than his best friend and rival Luke. Yuga's character is also fairly one-dimensional, he really just wants to play Rush Duels and be free. While Yuga's cards are powerful in Rush Duels themselves, the game mode isn't even available to western audiences after multiple years.
Yuya
Yuya's biggest goal was to bring "entertainment duels," a concept where duels became more about being a show for people to enjoy. Yuya began to face tougher and tougher opponents after introducing pendulum summoning to the world and eventually teamed up with rival Reiji Akaba to travel to different dimensions in order to stop the evil fusion academy.
Yuya's biggest flaw as a character and a duelist is that he's actually just a fourth of a full person. The strongest duelist, Z-Arc, split into four parts that included Yuya. Throughout the anime, the parts mixed and matched in a way that made it hard to ever tell what the real Yuya was like. His brightest point was the cards he introduced to the game: the incredibly powerful competitive Performapal and Pendulum Magician archetypes. Among them, "Performapal Pendulum Sorcerer" and "Performapal Monkeyboard" were two of the most game-defining cards ever.
Yugi
Yugi was just a normal high schooler until he solved the Millennium Puzzle and unlocked the soul of an unnamed Pharaoh. Together, the two went on dozens of adventures with the goal of saving people from danger and eventually restoring the memories of the Pharaoh's lost soul.
While Yugi had good moments in the final season and in Dark Side of Dimensions, it was the pharaoh Atem that dominated most of the original series. However, what Yugi lacked in early characterization and duels he made up for tenfold in his final duel against the Pharaoh. Aside from his dueling ability by the end of the series, Yugi did debut the incredibly impactful "Gold Sarcophagus" that was eventually put on the Forbidden & Limited List.
Yusaku
The Vrains protagonist Yusaku's story began when he encountered a strange virtual being known as AI, an aptly named artificial intelligence with incredible powers. AI turned out to be one of six Ignises, a special breed of artificial intelligence that was being hunted by a man named Revolver.
Yusaku is one of the most powerful duelists in the franchise, his biggest obstacles being AI, Bohman, and Revolver. Yusaku didn't have much character development in the traditional sense, but the way he warmed up to AI throughout the series was endearing to see. While not every Yu-Gi-Oh! fan knows Yusaku's most iconic cards due to how new they are, competitive players will know just how powerful his ace monsters "Firewall Dragon" and "Accesscode Talker" were.
Yuma
Yuma begins his journey as a protagonist after discovering Astral, an amnesiac alien who for some strange reason is an expert in dueling. Yuma's goal becomes to collect all 100 number cards, a species type of XYZ monster that contains fragments of Astral's lost memory.
Zexal is a polarizing anime in the community, partially due to how different in quality the first and second half is. Yuma parallels his own show in that regard, increasing in dueling ability and development as the series goes on. However, in season 2 Yuma is a top-tier anime protagonist, and his relationship with Vector is one of the best in the franchise. Yuma also brought out some cards that have impacted the meta throughout the years like "Number F0: Utopic Future" and "Gagaga Cowboy."
Yusei
Yusei Fudo was the protagonist of 5DS, a series starring a group of five chosen duelists called the "Signers" that gathered to stop the world's evil. Alongside his fellow signers, Yusei does his best to save Neo Domino City and the Sattelite where he was born.
Yusei was a talented and strategic duelist that dominated most duels in the series. Yusei's development was stagnant for most of season 1, but Yusei did have a strong character arc after a blowout loss to his old friend Kiryu. Finally, while some of Yusei's cards are overrated today, he also had timeless monsters like "Stardust Dragon" and powerful cards with a lasting meta impact like "Doppelwarrior" and the currently forbidden "Level Eater."
Judai/Jaden
Judai Yuki (called Jaden in the dub) attended an academy specifically designed for kids to improve as duelists. While there, a wide variety of antagonistic figures did their best to disrupt Jaden's peaceful high school life.
The protagonist of GX didn't start out as one of the strongest duelists in the series, but he ended up there after multiple arcs of development and a few deck swaps. No other protagonist in the franchise matched what Jaden went through during his time at duel academy. Jaden brought incredible spell cards like Super Polymerization to the game as well, a card that's seen limitless competitive play throughout the years. Not only that, Jaden's HERO archetype has had dozens of competitive iterations throughout the game's history.