How do the Mayship stops if May has the anchor? Because the Mayship is an airship, it doesn't need an anchor. Plus, May carries a different anchor than the one her ship has.
After Sol steals the Fireseal from the Sacred Order of Holy Knights, he doesn't even show even a hint of guilt at Ky's anger regarding the theft, or even an attempt to explain to Ky that he needs it to kill Justice. This is because Sol actually spent decades creating it along with all the Outrage pieces like Ky's Furaiken to combat Gears in the first place. Or in simpler terms: he owns them. And on that point, it's everyone else who's stolen his work and/or using it without his permission, such as Anji Mito with Zessen.
Gears and their stuff
How come Gears are created to grow fast that they become Jail Bait at 3 years old? Gears are treated as objects, specifically, weapons. If they need whole 18 years to mature then it wouldn't be practical to create them at the first place.
Command type Gears being female, passing their powers to their daughters and being the mothers of half human hybrids. In real science, mothers pass mitochondrial DNA to their daughters only. This could explain the reason why Sin is more like his father than his mother. And Gear mothers are more suitable than human mothers in cross-breeding, since human mothers cannot sustain abnormal fetuses that can probably summon a magical fireball inside the placenta.
Bridget getting recruited by Jam as her waitress/waiter. Jam had always wanted to recruit a blond, beautiful, blue and white clothed boy to serve her, and she has consistently failed to force Ky. Now gets a boy that fits her criteria, who attracts even the male customers.
In the Guilty Gear X anime trailer, the captions ask "why do you fight?" Before Sol, the word "Justice" appears and before Dizzy, "Sin" appears. If this is intentional, that would've been a deep cut, showing that Sin as a character was planned for years ahead of Overture.
At first, the abilities of Zato, Millia, Venom, and Slayer seem like pure Rule of Cool... but then it hits you: they have those powers because they're assassins. They're armed and ready to fight at all times, while remaining completely inconspicuous.
One of Ky's notable visual features is his belt buckle, which has the word "HOPE" inscribed on it. And in the XX drama CD, the event of Ky's death in the original timeline is referred to as "the day the hope of the world crumbled".
Ky never seems to age. He also has to wear his hair longer than he used to, since it keeps growing back faster than he can cut it. As revealed in Xrd -SIGN-, him being a Gear might have something to do with that.
No wonder Bedman's a Motor Mouth; when he's fighting in the real world, he obviously can't do any trash-talking since he's in a coma. His rambling in places where he can talk make up for that.
Chipp's usage of glasses from Xrd onward. While it does help with the whole "Presidential" look he's going for, it is also incredibly common for people with albinism to have vision problems due to a lack of melanin in the eyes. He's also having to deal with a lot more paperwork than he used to, back when he was a solo ninja doing his own thing.
Acquiring the Forbidden Beast. It's stated that it requires you to sacrifice what you treasure most. Zato lost his eyesight and it is unknown what Millia lost. Then what if you love your Biggus Dickus? Then it will probably be cut off.
I-No's time trolling. She can go back to the past as many times as she want and change ANYTHING. She practically controlled reality and make things better, making all the characters look like Ungrateful Bastards whenever they fight her.
If it weren't for Ky attempting to save I-No while she idly watched him with amusement, he wouldn't have died, and the original timeline wouldn't have fallen into disarray. That arguably makes things more frightening.
In Xrd, I-No's stage, "Babylon in five years", is a deserted ghost town devoid of color. At first, one would think that the name refers to the passing of time between XX and Xrd. However, I-No is also capable of travelling through time and taking others with her. As shown in Xrd -SIGN-, Babylon's inhabitants got annihilated at the end of Sol and Ky's arcade mode.
According to Dizzy's Instant Kill in Xrd -REVELATOR-:, her power is capable of causing a explosion on level with a nuclear bomb. Necro fires a deadly ball of energy at the opponent, in which Dizzy narrowly stops by tackling Necro. While it still fires, it almost hits the opponent. But this near-death experience makes the opponent give up the fight on the spot. Now imagine Necro suddenly losing his shit in a heavily populated area.
Chipp's lack of intelligence is often treated humorously in-universe. But considering his severe drug usage in the past, it's entirely possible that it resulted in some form of lingering brain damage.
Alternatively, considering the fact that he grew up as an inner-city orphan, it's possible that he's never gone to school.
May summons dolphins and whales, though the Jellyfish pirates actually travel on air.
Again on May, her IK has everyone of her female friends joining her including Dizzy. Setting a mirror match aside, Dizzy can be seen flying along with the crew even if she's your opponent.
Story modes in general. The first stage you're in China, then to London, then to Hell, then to Paris...
Sol's bad ending Accent Core. In both endings, he is transported back in time by I-No where he fought his younger self, Ordel Sol. After the fight, I-No kills his younger self. Actually, it makes you wonder in the first place why Sol just fought a lookalike without thinking. In the bad ending, where Sol dies, why would you die if your younger self dies? Then who fought your younger self? Why did you exist in the first place?
Order Sol: I'll crush you!
In Overture, Ky's servants dropped from the sky.
It may be his main source of appeal, but why does Bridget still wear nun clothes if he wants to be so manly?
Because of Rubber-Band History where multiple timelines can possibly exist like one big happy family. If I-No changes the past, she doesn't necessarily erase the former timeline, just like what happened in the Drama CD.