Arc Fatigue: Mona first meets the man she's crazy about, Lucas, in November 2003. Lucas is also crazy about Mona. For eight years running, it's hit and miss, hit and miss, almost this and almost that happening— and not even a real date in all that time. One kiss in eight years. Despite Lucas being described as her future "true love".
Fridge Logic: Most of the story. The anther has strangely never been called out on it. For a good example, see Refuge in Audacity.
An even better one occurs in Chapter 36. Jack, still recovering from a huge hit, can't feel his legs. He deduces that since his legs are fine, his spine is just shaken up. As soon as everyone goes to mobilize, he's apparently fine enough to use a pedal-operated vehicle that goes in excess of 300 km/h.
Genius Bonus: Yusei apparently understands that time is the 4th Dimension.
Ho Yay: Several characters relationships come across this way, but Judai/Yusei and Taiyou/Kyojo are the strongest.
I Am Not Shazam: Before an official name existed for the Three Emperors of Yliaster, they were referred to as "Infinity" as though that were the name of their organization.
