Yugioh had several planned things throughout the anime and real-life TCG but was eventually scrapped or realized. It also contains things that we, the audience, felt needed an explanation. In addition, the game and anime also include several speculations. I thought it would be fun to make a compilation of them.

Seven-Armed Archfiend – DM

In episode 13 of Yugioh DM, this card appeared in Bakura’s flashback. The card has an ATK/DEF of 666. Its ATK and DEF value obviously refer to the devil’s number. This monster never appeared in the manga. It was created specifically for the anime in that specific flashback. Seven-Armed Archfiend never made another appearance in the series. However, it did appear in the Yugioh Spinoff series, Capsule Monsters. So what was the whole point of this monster? It seems like the card was planned to be focused on more but was dropped early on for whatever reasons.

Kaiba and Kisara - DM

Accordingto Takahashi, the creator of Yu-Gi-Oh!, Kaiba and Kisara (Blue Eyes White Dragon) ’s relationship and story in the Yugioh storyline wasn’t what he had initially envisioned. The final product of their story resulted from executive meddling and rushing to meet the deadline. Originally, Takahashi wanted Kisara and Kaiba to have a closer relationship. Her eventual death would’ve resulted in Kaiba rebelling against the pharaoh, which is a plot that was also cut/rushed.

Kaiba's Rebellion – DM

Early in the series, there were constant visions of Kaiba duelling Atem back in ancient times. In those visions, Kaiba was rebelling against Atem. The visions were greatly hyped up, and it seems like a significant plot point. When the battle was finally shown, it turned out that it wasn’t that important. In the actual battle, Kaiba was possessed, contradicting the original visions, where Past Seto was clearly an enemy.

According to Takahashi, he intended Past Seto and the Pharoah to be enemies. His rebellion was the result of Kisara’s death. However, he aborted this plotline due to executive meddling and rushing to meet deadlines. This ended up contradicting everything shown before.

As for why Past Seto would rebel because of Kisara’s death? Perhaps initially, Atem was a ruthless Pharoah who caused Kisara’s death, causing Seto to rebel. This aligns with Atem’s initial brutal strategy of mind-crushing his opponent and playing traumatizing penalty games with his victims.

Kaiba having the Millennium Rod - DM

When the Tablet of Lost Memories first debuted, Kaiba held a normal staff. However, Kaiba having the Millennium Rod became a major plot point later in the series. This resulted in the tablet changing from Kaiba holding a regular staff to holding the Millennium Rod. What was the original plan if he was never supposed to have the Millennium Rod, or was it just because the Millennium Rod's design hasn't been finalized yet?

Fire Dragon – GX

In the first GX anime opening, a prominent snippet shows Bastion with his Water Dragon and an unknown Fire-Attribute Dragon. Judging from the fact that it appeared in the anime opening, it was clear that the writers planned for Bastian to have this monster. In fact, he was built up to have six different Decks based on different Attributes. It can be theorized that the Fire Dragon would have debuted in his Fire Attribute Deck. In addition, since there's a Water Dragon and Fire Dragon, were there meant to be a dragon based on the other attribute (Wind, Light, Dark and Earth)?
Either way, Bastion dueled sparingly in the first season on GX (only three times).

Six Attribute Decks & Bastian - GX

In episode 12 of Yugioh GX, Bastion revealed six different decks, focusing on different attributes. However, throughout the Yugioh GX series, only the Water and Earth Attributes Deck were shown. Judging from the Anime opening, where a Fire Dragon appeared alongside Bastion, it's implied that he was initially going to use a Fire Attribute Deck as well. Either way, we never got the Fire Dragon or got to see his other attribute decks.

The character, Bastian, himself is another scrapped plan. In GX's first season, Bastion was hyped to be an essential character, being the true rival of Jaden. However, during the Seven Shadow Rider's arc, he was quickly diminished into a comic relief character. This created a domino effect, causing him to be mostly forgotten in Season 2, despite being part of the main cast. Bastian was the only main Society of Light member who never got to fight Jaden. He only made a few minor appearances in Season 3, where again he was left out of the main plot before being written out permanently. Bastian didn't even make an appearance in Season 4, except for a vague silhouette of him shown by Nightshroud.

Bastion’s Spirit Monster – GX

During Season 1 or Season 2 of GX, Bastion found a card that contains a spirit. One would expect that this would be expanded upon, considering how spirits are quite prominent in the series (e.g. Ojama and Winged-Kuriboh). However, it was quickly abandoned after that scene, and it was never explained again.

Abandoned Dorm – GX

One thing that bugged many viewers was the Abandoned Dorm plotline in Yugioh GX. The Abandoned Dorm was hyped a lot during the first half of Season 1, which has tons of filler. In addition, many of the main and core characters had connections with that dorm (e.g. Banner, Alexis, Atticus, Chancellor, Kagemaru, etc). However, The Abandoned Dorm was quickly forgotten after Atticus debuted. Only to be brought back in Season 4, where it seems like it would finally get some closure. However, since GX Season 4 was rushed, the Abandoned Dorm was partially resolved at best. We never got to know why Kagemaru or Banner lured the students to the dorm, why the students disappeared, and tons of other stuff.

Planned Mystic Archetype – GX

Blair was a one-shot character in Season 1 of GX. She returned in Season 2 with a new deck called "Mystic" and became a recurring character afterwards. However, after becoming part of the main cast in Season 3 and 4, she never dueled in a one on one duel again. This prevented us from seeing more from the Mystic Archetype. Some may argue that the archetype was just a one-off filler archetype like her Maiden in Love Deck. However, the spell card "Mystic Revolution" text has the following effects:

"Tribute 1 face-up "Mystic Baby Dragon", "Mystic Baby Knight", or "Mystic Baby Magician" you control. Special Summon, from your hand, Deck, or Graveyard, 1 monster written in the card text of the selected card, ignoring the Summoning conditions."

This shows that the writers planned more from this Mystic archetype. We never got to see Mystic Baby Knight or Mystic Baby Magician or their grown-up counterpart.

The Light of Destruction – GX

The Light of Destruction is arguably the main antagonist of Season 2 of GX. However, the anime never told us what happened to it. When Jaden defeated Satorius, only parts of the Light of Destruction was destroyed. It even appears again in Season 3 in the other dimension, where it is implied that Jaden and Yubel will fight it. However, it never happened. In addition, the war between Light of Destruction and Duel Monsters was never shown or explained either.

Jesse as the "Chosen One" - GX

From the first episode where Jesse debuted, the writers did everything to hype up that character. They did so much hyping that they eventually coined the term that Jesse was the "Chosen One". However, the anime never told us the Chosen One of what? Chosen One of Crystal Beast? For the Rainbow Dragon? Chosen One to be a pawn of Yubel? To be Jaden's best friend? Furthermore, in Jesse's debut episode, Jesse and Jaden stated that they feel like they've seen each other before, implying some backstory or connection. However, nothing ever came from that statement. It became a mere throwaway line. 

Sacred Beast Locking – GX

It's just strange that their origin wasn't explained despite being important to the plot. The sacred beasts were the evil counterparts of the Egyptian God Cards. It was stated that they were so evil that they had to be locked away. In addition, they were also extremely powerful and possessed a lot of power. However, the anime never bothered telling us how the cards were created. Were they failed copies of the original Egyptian Gods? In addition, it was never stated how they got sealed away in the first place and why they could absorb duel spirits.

Rushed Season 4 – GX

We all know that Yugioh GX Season 4 just didn't feel right. It wasn't bad, but it felt lacking, considering it was the final season. There were many loose ends, and it was only half a season. It felt kind of rushed, and that's because it was.

The season was going to have more episodes. However, rumors ranged from Jaden's voice actor quitting, getting fired, or Konami rushing out 5D, causing the final season of GX to be cut short. There were many speculations that the GX Tag Force 3 game featured many plot points that were supposed to be in the final season of GX. For example, Trueman's plot was more elaborated in the game compared to the anime. If that's true, we would've possibly seen Bastian appear again, joining Trueman's side.