Within moments of his reveal, Reiji Akaba has been christened by many as "Hipster Kaiba", especially when he wears that trendy hoodie while eavesdropping in episode 9. Just take one look at him and no further explanation is needed.
Yuya has been nicknamed "Tomato Head" by many. Once again, such a name needs no explanation.
Yuya being sad, uncomfortable or upset. Wilting/rotting tomato.
The Dark Duelist Yuto is also referred to as the Goth Duelist, Edgeplant, Edgeyuya or Dark Yuya.
Immediately after his appearance without the helmet is revealed, fans has been calling Yugo "Banana Head" due to his bang.
The alternate Yuzus are known as Yuzu (Fusion Yuzu) and Edgeyuzu (Ruri)
While it's not normally obvious, as soon as Reiji starts hamming it up, anyone who watched the previous series will likely get IV flashbacks. Before them, their seiyuu voiced the minor character Dick Pitt, one of the Dark Signer Drones from 5D's.
Real-Life Relative: The seiyuus of Yuto (Manpei Takagi) and Yugo (Shinpei Takagi) are twin brothers.
Teasing Creator: The showrunners seem to know exactly what will annoy the fans and lampshade or address it. Examples include:
Yuya's Ass Pull of getting his Pendulum Monsters mid-duel is considered as such in-universe.
Futoshi, who is considered The Scrappy by many, and is a wee bit of a Fat Idiot, usually gets a few derogatory comments thrown his way.
Kyuando is another scrappy who earned attention from the creators. While Yuya's other opponents during the Qualifying arc (Michio, Mieru and Gongenzaka) appear in the second opening, Kyuando is left out.
Your Size May Vary: In episode 24, Hidekazu Ebina (the episode's animation director) said that he intentionally made Yuto taller than Yuzu despite that he's supposed to be shorter than her. His reason was that this was supposed to give Yuto's exposition a sense of seriousness.