In the duel against Jaden while representing North duel academy Chazz refuses to use the cards his brothers gave him why? Because he has already seen the result of taking a bunch of good cards and mashing them together the first time he lost to Jaden.
Why did the Winged Dragon of Ra obey Jaden even though he doesn't have an Egyptian heritage? Because Jaden's opponent, Franz, abused it and treated it like a slave, so fighting on Jaden's side would enable it a chance to get back at its owner!
It's also possible the Winged Dragon of Ra could sense that Jaden was the Supreme King reborn.
Alternatively, Ra noticed that Jaden possessed Winged Kuriboh, and recognized that this meant that Jaden was favored by Ra's true Master (Atem), or at least his master's long-time partner (Yugi).
Most of Aster/Edo's Destiny Heroes have names that start with D. Most of the cards' names were changed for the dub; Diehard Guy was renamed "Captain Tenacious."
As noted under Punny Name, Yubel's name may trace back to several forms: "juwel" (you-vel), meaning jewel in German; "jubel" (you-bell), meaning happy or joyful in the Scandinavian languages; or "übel", meaning evil. Yubel discovers that there is no happiness for them in being evil, and that their true destiny is to help Judai to defeat the Light of Destruction, not to take him away from his new Scandinavian (or possibly German—the spelling inconsistencies make either a possibility) friend with a jewel-based deck.
Daitokuji/Banner may be foreshadowing/making references to the Society of Light arc (somewhat) and especially the Darkness arc. His line, "Everything in this world is born through one substance, which changes variably, creating the sky and earth." This is also what Darkness' "The world was born from a single card..." speech is based on. Banner's card, The Philosopher's Stone - Sabathiel foreshadows the final opponent of the last arc, Darkness, who is the representation of humanity's despair. The hermetic angel Sabathiel is the Angel of Saturn, a planet which symbolizes Nigredo. The Nigredo phase has been interpreted by Carl Gustav Jung as the period of despair.
When you think about it, a lot of things about GX that initially made no sense or just seemed weird suddenly make more sense. For example, the community at tv.com found a lot of the Freudian Excuses ridiculous — Martin making a Deal with the Devil just because his parents got divorced, Fujiwara being overcome by Darkness and orchestrating the Assimilation Plot just because his parents died... In retrospect, maybe they were supposed to look ridiculous and show how having some normal sadness or Parental Issues in your past is a lame excuse for causing The End of the World as We Know It. Even Edo thought him risking his life to protect Ekou made no sense — deliberately showing how absurd The Dulcinea Effect is? And, of course, there's Fujiwara needing to use Mind Control to get characters to Remember the New Guy? and Manjoume's Break the Haughty arc going so far that it becomes detrimental to him. Basically, the more audacious and over-the-top this show's use of a trope is, the more likely it is that it's actually a Take That! at the trope or its genre.
You may have noticed that whenever people reference Yugi in GX, it's always referring to Yami. At first, it seems shallow, since it references solely his actions in the original series without taking in consideration the time gap between DM and GX. Later on, you may realize that this was Yugi—in the time span between the two series, Yugi had changed dramatically from who he was in the start of the entire series. His Yami-like appearance was an artistic representation on how he matured. This to the realization why his face is obscured during the present day—he does look like Yami, but hiding it blocks non-Brilliance'd viewers from thinking Yami might be back.
The Entire reason that Yugi gives Jaden the "Winged Kuriboh" Card at the start of GX is because Yugi knew who he was, as well as the fact that he would use the Kuriboh cards because of the events of Yu-Gi-Oh!: Bonds Beyond Time. This is because in the film Jaden uses The Flute Of Summoning Kuriboh. For Jaden, he is meeting Yugi for the third time, but for Yugi, they are meeting for the first time. (The order being "GX:1", "GX:180", "The Movie" for Jaden, but for Yugi "The Movie", "GX:180", "GX:1") This explains why Yugi would give a random duelist one of his cards, as well as why in episode 180, Yugi (the one Jaden duels, in the past) knows Jaden's name, without being told. It really is a brilliant Stable Time Loop.
At first glance it seems like the dub names were chosen at random, but upon realization that all of the first-year students (Chazz, his cronies, etc.) who start off in Obelisk Blue must have gone to DA's prep school, all of the preppy names make sense.
Before going to Domino City, when Sartorius is coldly confessing to Aster that their friendship is only a part of destiny, like everything else he taught him, and Aster's purpose was served by brainwashing members, Sartorius has tears running down his face. Strange for the Big Bad to be crying while displaying his Manipulative Bastard plan, but later on it's revealed Sartorius was under Demonic Possession by the Light of Destruction and it was the real Sartorius crying as the Light cut off his friendship with Aster.
Yubel is an exaggerated Violently Protective Girlfriend during Jaden's childhood because she has been the guardian of the Supreme King's vessel for several unknown lifetimes. Who knows what experiences Yubel has encountered trying to protect him from people pretending to earn his trust, or even considering the Supreme King himself can turn out to be evil, Yubel didn't take any chances with whatever Jaden or his friends might believe his best interests are.
After Zexal's reveal of the Numeron Code, Darkness/Nightshroud's speech about the origins of the universe as represented by a single card becomes much less metaphorical in retrospect.
Yubel has a right female side and a male left side, which is probably inspired by a saying in Asia "male on the left, female on the right".
In the last two episode of of the show, Yugi says to Jaden that he will challenge the most powerful duelist to which Jaden asks if he is stronger than Yugi. one might think that Yugi is referring to Atem since he's always with him (and the fact that he has the God cards) but he actually might be referring to the combination of him and Atem.
Judai not knowing what a "fiance" is makes a lot more sense (and shades into Fridge Horror) once you know that a significant portion of his childhood memories were erased.
Judai's favorite card is a mix between a man and women, part dragon, has an effect that deals damage based on the opponent's monster's attack and through a source of light becomes much more powerful and vicious, before it gets replaced by Elemental Hero Neos. Are we talking about Yubel, or Elemental Hero Flame Wingman?
At first one may find it odd that Judai's designs for Kaiba Corp's contest were the ones sent to space; after all his drawings weren't precisely the best. Until you remember that Seto Kaiba said that he would handpick the winners. Why? Because Seto's little brother Mokuba once did a similar quality drawing of a Blue-Eyes White Dragon for him during their childhood so he picked those designs because of nostalgic reasons. May also count as Heartwarming.
The names of the different dorms were chosen by Kaiba, which is why Obelisk is at the top, since it was Kaiba's god card. It also explains why Slifer is at the bottom and Ra in the middle, because it was Yugi's original god card and Kaiba doesn't like Yugi and is apathetic to Marik.
When one looks at the three dorms, it actually makes sense that Kaiba would set them up not just because he wants to spite Marik and Yugi (given they're put under Obelisk, aka him), a lot of the duelists in the dorms represent people that fit their best skills, at least in important roles;
For Obelisks, the skills are refined to the point of being at the top of the batch and thus have a lot of powerful cards (like Zane and later Syrus), just like Kaiba did at first. However others like Alexis or Chazz use weaker cards with powerful effects, which is also another type of strategy Kaiba uses in conjuction with his powerful cards.
Marik is a master strategist and tends to think ahead, which is why many Ra students like Bastion or Hassleberry seem to rely more on fine-tuned stategies than anything else.
And finally Yugi himself is a bit of an underdog at first, starting out with what was basically a mishmash of weak cards that balanced each other out and climbed up the ranks from the bottom. Now, why would that sound familiar considering who the main character is? Not to mention both Jaden and Yugi are Magnetic Heroes, being able to make friends with former rivals and get many people on their side.
Not only that, this can be taken a step further when examining the abilities of the Egyptian Gods themselves and how they relate to the students.
Obelisk: In terms of raw power, the strongest of the three with base ATK and DEF of 4000, the same way that in terms of raw power Obelisk Blues have the best decks and the best cards at their disposal. Furthermore, Obelisk can sacrifice two monsters to destroy all monsters the opponent controls, which mirrors the way that Obelisk Blues are willing to pay any cost if it means assured victory, like Season 1 Manjoume willing to throw as much money as he could into his deck. Obelisk Blues crush anything in their way, but lacking finesse can be outplayed by other, more thoughtful combinations assembled of weaker cards beneath their consideration.
Ra: Ra represents the most variance in power of the Egyptian Gods, but has the most tricks at its disposal. Its (anime) effect of gaining power equal to the combined power of the monsters used to summon it reflects the wide range of talent of their students; with the right combination of cards they can easily surpass Obelisks in power and skill, but the wrong combination and they're as mediocre as Slifers. Ra's ability to reduce its controller's lifepoints to 100/1 and give them to Ra is another facet of duelists such as Daichi who is willing to put his all into his deck; giving up all but 1 lifepoint is perfect efficiency. Similarly the ability to pay 1000 lifepoints to destroy a monster shows deliberation by weighing the value of lifepoints vs. field advantage. Ra Yellows have multiple tools at their disposal to win, carefully determine the best ones to ensure victory, and can vary wildly in terms of capability.
Silfer: Slifer represents the most raw inherent potential of the Egyptian Gods, multiplying its strength by 1000 with each draw. While many Slifers are slackers who don't try, there are also those like Sho who work hard to improve themselves and grow more powerful over time. Having the weakest decks, Slifers will rely on one of two things: lots of weaker creatures working together like in Sho or Judai's decks, or very basic decks that summon big creatures and attack head on, with less strategy of the higher dorms, like Hayato. Slifer's attack reduction ability reflects both of these paths, either by using combos to reduce monsters with over 2000 power down to something manageable or steamrolling over anything with less than 2000 power. Slifer has infinite potential and when it becomes strong enough is nearly impossible to stop, or even oppose, but must be built up from scratch, just as the Slifer Reds start from the bottom and must improve themselves.
Some have complained that Judais Freak Out and its aftermath in Season 3 comes out of nowhere and is at odds with the fact that he had already had to play Duel Monsters to decide the fate of the world in the first two seasons... except that, before Brron sacrificed his friends, Judai had never gotten genuinely angry or upset.
During Jaden and Bastion's duel, many have pointed out that while Cursed Seal of the Forbidden Spell prevents the use of Polymerization, it doesn't for alternative fusion methods, mainly Fusion Gate (we're not supposed to know that Miracle Fusion is a thing yet). This seems like an oversight on Bastion's part but it makes sense, if Jaden did use Fusion Gate, Bastion could have just used a simple spell destruction card to stop it and knowing Jaden's tendencies, he only put one Fusion Gate in his deck, assuming he didn't cycle it out. In addition, Jaden has plenty of cards to recycle Polymerization if he needs to so striking that card down is still a really good play.
Jaden's third duel against Aster actually mirrors Zane's duel against Aster. As both Zane and Aster are facing familiar yet brand new Heroes. Jaden and Zane both had to recover after taking a significant amount of damage (Zane from Power Bond, Jaden from taking multiple direct attacks). Both Zane and Aster are duelists that have defeated Jaden before. The most notable similarity is in how Jaden wins the third match, and in how Aster defeats Zane. Both of them attack with a monster that they believe will overpower the opponent. However, Aster activates a card that allows him to send more Elemental Heroes to the graveyard to power up his monster, allowing him to defeat Zane. Aster falls to this in his third duel against Jaden, and as Jaden points out (in the dub version at least), Aster's downfall was thanks to himself as well. Aster destroyed Jaden's Spell Calling, which allowed him to power up his Hero monster and overpower Aster.
One of the cards Yubel uses as fusion material for Super Fusion God is Lava Golem, a wonderful card to use in a Yubel deck. (A 3000 attack monster that summons itself to the opponents field in exchange for giving them burn damage.)
When the Sacred Beasts return in season 3, why weren't they shown draining the power from all other cards around them as they did in season 1? Well it takes far more energy for a duel spirit to take physical form in the human world than in the spirit dimensions. It's only natural they'd be less hungry.
The whole "sent to the stars" thing in season 3 might seem like silly 4Kids censorship, but it does make some sense. After all, that's literally what Jaden did to Yubel when he was a kid. He asked KaibaCorp to send Yubel into space hoping Yubel would absorb the cosmic rays like the Neo Spacians did where they instead came into contact with the Light of Destruction, driving Yubel insane. In the dub, Yubel is now targeting his friends and anybody who loses a duel in the alternate dimension explodes into stardust. For Yubel, it's poetic revenge. Beyond that, Yubel desires to unite the 12 dimensions, which would've destroyed everyone and everything except themselves and Jaden, similar to how stars work in real life when they explode at the end of their life cycle and a new star is born out of the remains after pressure is applied over time.
Not to mention, it actually makes more sense than just saying they died. After all, at the end of the season it turns out that they were being sent to another dimension instead, so they really were sent somewhere else.
There's a noticeable difference between how Zane/Ryo and Syrus/Sho use the card Power Wall, namely in regards to how they treat the cards they mill using its effect. Zane disrespectfully throws the cards to the ground, while Syrus just sends them to the graveyard normally. No wonder the deck was causing Zane's heart problems, seeing as he was constantly disrespecting them by treating the cards like trash. Noticeably, after Syrus starts showing the deck itself more respect, it stops inflicting similar problems to him.
How come Jaden never found out he won the Kaiba Corp Contest? It's because he got his memories all messed up from the shock therapy he received as well as the constant trauma from the Yubel nightmares.
In the fourth episode of the first season, Duel Academy has an entire military transport just to protect its shipment of rare cards. It's validated when the captain mentions they've had to fight off "mecha-triggers (something like that) and attack subs". People probably died. Considering the fights people get into using them, this is a world where wars may very well be fought over trading cards as weapons.
Becomes worse after watching Arc-V and Academia. It's not hard to imagine that the Government was in on or endorsed the attack on Heartland.
Also becomes worse when you remember the Rare Hunters from the original series. They are a dangerous group of raiders... who's to say that, even with Marik reformed, they aren't still around?
Given Majoume had them in his nightmare in Season 4, they probably aren't just still around, but infamous and major boogeymen.
Take a look at the future Darkness/Nightshroud shows Judai in their final duel after watching 5Ds. Seem familiar?
In season 4, Ryo is twenty years old and has a severe heart condition. His eighteen-year-old brother (who has no medical knowledge) appears to be his only advocate. Where are their parents, and what kind of life can they possibly have going forward? Ryo might say he wants to start over and duel again, but his health is obviously still a major concern.
Manga: In the final chapter, Ryo is shown in his "Hell Kaiser" outfit from the anime. What happened?
It's a really good thing that Rainbow Neos seemingly managed to get rid of all of Trueman's clones when it emerged during Jaden and Jesse's duel with Fujiki. After all, Trueman both draws his power from, and is composed of, cards tainted by the negative emotions of their users. The thought of him manifesting from the decks of characters like the Dark Signers, Z-ONE's crew,or even the average Number Holder is... frightening, to say the least.