Adorkable / Yu-Gi-Oh!

• Yugi Mutou, the actual one, not the Superpowered Evil Side. He's a slightly dopey, socially awkward kid whose deepest wish in the first chapter is just to have a few friends. He gets them though, because people finally start seeing and appreciating his Incorruptible Pure Pureness.
• Serenity Wheeler. She plays games in the video games and is absolutely adorable. Ditto for Mokuba Kaiba.
• Ryo Bakura also qualifies, if he isn't more so. He's the shy kid in the sweater who's obsessed with games of all kinds and has very little friends. Too bad he was downplayed in the anime. And again, this is the REAL Bakura we're talking about. The Spirit inside him is... less adorkable.
• Syrus Truesdale from the spinoff series Yu-Gi-Oh! GX, given that he looks a lot like Yugi with blue hair and little round glasses. It gets to the point where fans joke that Yugi is his father/mother.
• Judai Yuki, the main character from Yu-Gi-Oh! GX also qualifies, specifically at the beginning of his journey. He's a really happy and bubbly teenager, who is always smiling and very charming with his clumsy quirks, even when the odds are against him and he sometimes doesn't get what's going on or realizes it is too late, he stays kind and happy.
• Jun Manjoume, from Yu-Gi-Oh! GX is the rather odd cute rival of the series, who is a little grumpy but also quite clumsy as he finds himself in some very weird situations. He serves as the comic relief.
• Carly Nagisa, from Yu-Gi-Oh! 5Ds. A clumsy but cute Intrepid Reporter, who awkwardly stumbles her way into Jack's heart and is happiest when she's cheering on her friends. The Opaque Nerd Glasses and Thinks Like a Romance Novel attitude are just icing on the cake.
• Team Taiyou, also from 5D's. Most of the WRGP finalists are elite duelists with expert decks and strategies, and have the attitude to go with them. Taiyou, on the other hand, are just a couple of poor, friendly guys from the country who eagerly want to prove their worth to the world. The hijinks that ensue when they try to put together a bike and deck are hilariously endearing.
• The best example from Yu-Gi-Oh! ZEXAL is III, a Rose-Haired Sweetie who loves ancient artifacts and civilizations. When he sees everything Yuma got from his father's adventures stashed in his room, he quickly starts geeking out over everything there. It means all the more to him considering his deck is based around such things.
• Yuma Tsukumo from Yu-Gi-Oh! ZEXAL starts as a rather annoying character, but certainly has this charm too, as he often really misunderstands social cues and wants everybody to be friends, which is heartwarming. He ends up in situations where he hurts himself accidently and makes an idiot out of himself, but you can't bring yourself to hate this child for it.
• Yuya Sakaki from Yu-Gi-Oh! ARC-V is a jokester and a very big crybaby but ultimatively just wants everybody to be happy, which is cute and endearing. Even tho his message to the world is sometimes a tad bit too much, he has his pure moments, where he forgets how to summon, accidently falls from his monsters or smiles like there is no tomorrow over getting some tasty food.
• Ai from Yu-Gi-Oh! VRAINS is one of the comic reliefs of his series. His humour reaches from cheeky to very cheesy. At the beginning he often can't decide which side he wants to take which results in some hilarious scenarios. During the series he blows kisses to the main character, tells him that he is cute and even scratches his head while awkwardly declaring that he was dumped by him. He even starts crying when Yusaku says that Ai is indeed his partner for the first time. He instantly adds, that he's of course Yusaku's best friend. Ai also loves soap operas. In season 3 he even has his own punny cards. Ai is always just a tad bit too much to take. But that's what makes him likable.