There are a lot of allusions to various other Yu-Gi-Oh! series within several episodes of Yu-Gi-Oh! ZEXAL. Despite this, there are no actual plot points in ZEXAL relating to the other three shows, which differs from them (as the other three shows had clear points of continuity and direct references with each other).
Tori Meadows has a lot in common with Téa Gardner, wherein both are kind-hearted, strong willed and supportive. Both cheer their friends and stand up for what they believe in and will do anything to help their friends. Both are shown to get easily jealous when others (Mai Valentine (initially), Vivian Wong and Rebecca Hawkins for Tea, with Cathy Katherine for Tori) flirt with the one they love (Yugi Muto for Tea and Yuma Tsukumo for Tori), sometimes to the point where they have an explosive outburst. Despite their strong bonds with their friends, they are not above keeping the others (mainly Joey and Tristan for Tea; Bronk, Caswell, Flip and Yuma for Tori) in line when they get out of control or act foolishly. Both are protective and fiercely loyal to the one they love and both admire their unwavering will and determination. Both are shown to worry about the safety of the one they love when they are in danger. Both show an extremely strong resolve and can be unrelenting at times.
Yuma and Tori's relationship shares many similarities with Yugi Muto and Téa Gardner's relationship.
Don Thousand, the God of the Barian World, was defeated by Astral thousands of years ago and sealed away, much like Zorc Necrophades was sealed away thousands of years ago by Atem.
The Millenium Puzzle, much like the Emperor's Key, was also purloined or taken away from the main protagonist on several occasions.
The final duel between Yuma and Astral is similar to the Ceremonial Battle. Astral used the "Numbers" and "Utopia" while Yuma used the "Syllables" and a new ace card: "Number F0: Utopic Future", just as Pharaoh Atem used the "Egyptian God Cards" and "Dark Magician" while Yugi used monsters with toy themes, monsters that grow over time and a new ace card: "Gandora the Dragon of Destruction". Both Duels resulted in the defeats and departures of Yugi's and Yuma's partners.
Kite Tenjo's will to protect his younger brother Hart is similar to Seto Kaiba's desire to protect his brother Mokuba.
The bond between the Tenjo brothers is similar to that between the Kaiba brothers.
Shark has a lot in common with Joey Wheeler, wherein both bully their respective series' protagonists, Yuma and Yugi, early on in the series, but then later become good friends.
Both were shown to love their sisters (despite any disagreements they ever had).
Joey kept a picture of his sister in his wallet, while Shark wears the rings his sister made for him as a reminder of their bond.
Joey often states that Serenity was his biggest inspiration throughout Duelist Kingdom and Battle City. Rio was Shark's inspiration to enter the National Duel Circuit and the World Duel Carnival.
Both entered to either ensure their sister was cured (Serenity)/avenged (Rio).
Bother were shown to be loving and loyal to their brothers (despite any disagreements).
Just as Serenity was close to Téaa, Rio was close to Tori.
Like Tristan Taylor and Duke Devlin, who developed crushes on Serenity after she recovered, Bronk developed a crush on Rio when she returned to school.
Flip Turner shares many personality traits with Weevil Underwood. Also, both cheat when they Duel by messing with their opponent's Decks beforehand.
Number 96 shares a similar role to that of Yami Bakura, an evil entity that dwells within an artifact which is important tothe plot. Also Number 96 is a part of Don Thousand just like Yami Bakura is a part of Zorc Necrophades.
It is the first tournament in Yu-Gi-Oh! anime history since Battle City to require participants to collect what are essentially pieces of a puzzle (in the WDC, Heart Pieces, which are needed to power the Duel Coasters; in Battle City, Locator Cards, which contain pieces of a map) in order to enter the final round.
Furthermore, during the second round of the World Duel Carnival finals, each Duel is held on a different field with its own unique characteristics, similar to the KC Grand Championship, and somewhat antithetical to Duelist Kingdom, where the finals were held in the castle on a normal field and the remaining Duels were on special fields.
Similar to how Seto Kaiba started the Battle City tournament to claim the remaining Egyptian God Cards, Mr. Heartland and Dr. Faker started the World Duel Carnival to claim the remaining Number cards.
Yuma and Kite's Tag Duel against Trey and Quattro is similar to Yugi and Seto's Tag Duel against Lumis and Umbra. Both Duels had the lives of the rival's younger brother at stake (Mokuba and Hart)
"Rank-Up-Magic Barian's Force" is similar to "The Seal of Orichalcos" by how the the logo on the cards appear on the foreheads of the people who use it, make monsters stronger by dark magic, used by the main antagonists and appear in season 4 of their respective eras.
Vector using an alternative name to gain the trust of Yuma and his friends is similar to how Marik Ishtar used "Namu" to deceive Yugi Muto and his friends and how Yami Bakura used Ryo Bakura as a masquerade to hide his true goals.
The way Vetrix used Hart as a shield against Kite is similar to the way Noah Kaiba used Mokuba as a shield against Seto.
The way Astral took the hit from Number 96 for Yuma and later Eliphas sacrificing himself to destroy Numeron Network is similar to how Yugi pushed Yami out of the way when Yami's soul was going to be taken by "The Seal of Orichalcos" and how Shadi sacrificed himself to save the Pharaoh from Zorc Necrophades.
Don Thousand orchestrating the death of the Seven Barian Emperors for his sake is somewhat similar to how Dartz manipulated some events just to recruit Raphael, Valon and Alister.
Before Dumon was absorbed by Barian World, he used "Sacred Shield" card to boost "Number C103: Ragnafinity", having trust in Marin. This was a similar scene when Kaiba activated "Wish of Final Effort" to boost Yami Yugi's Life Points before his soul was taken to the "Seal of Orichalcos".
Thief King Bakura sacrificing himself to summon Zorc is similar to Vector releasing Don Thousand.
Mr. Heartland's Duel against Kite is similar to Noah's Duel against Seto. Both rivals of the respective series were incapacitated by their opponents (Noah turned Seto to stone, while Kite fell unconscious partway through the Duel, due to the strain of the opposing attacks), while the main protagonists, Yami Yugi and Yuma Tsukumo arrived to take their place with the same amount of Life Points. The protagonists combined the rivals' cards with their own, and used the rivals' ace cards (Kaiba's three "Blue-Eyes White Dragons" and Kite's "Galaxy-Eyes Photon Dragon" in the second series and ZEXAL, respectively) to finish off their opponents.
The ZEXAL powers that Yuma and Astral use to combine into one are similar to the way Yugi uses his duel armor powers to merge together with his Capsule Monsters.
Both of the protagonists, Yuma Tsukumo and Jaden Yuki have energetic, cheerful and easy-going personalities but become very furious and serious when their friends are put in danger.
Both characters also sport red attire and are known to not do so well in school.
Astral and Kite's rivalry, at least prior to the WDC, is similar to Jaden's rivalry with Zane Truesdale, in that the protagonist loses the first Duel (almost loses, in Astral's case, as the Duel is interrupted) and ties the second Duel.
In episode 1, Yuma was rushing for being late for school at the start of the series is similar to Jaden rushing to the entrance exam, due to being late for it.
Later on, while Yuma continued running to school, he bumped into a Litterbot, causing his cards fall out from his messenger bag and scattered on the ground is just like Jaden collided with Yugi Muto, which also caused his Deck to be scattered on the ground while rushing.
In episode 17, Fortuno kidnapped some of Yuma's friends and placed them atop a pillar where Fortuno casts an illusion that they are standing atop lava; this is very akin to when Jaden first Dueled Nightshroud in a volcano by which beforehand, Nightshroud abducted two of Jaden’s friends, Syrus Truesdale and Chumley Huffington, whom are subsequently plunked in a protective globe in the vicinity around actual lava.
Yuma and his friends going to the Barian World to save Ray and later Yuma going to the Astral World to save Astral is similar to how Jaden and his friends went to the Duel Monsters Spirit World to save Jesse Anderson.
Yuma and Shark's Duel in episodes 61 and 62 has many things in common with Jaden's Duel with Chazz in GX episodes 87 and 88. Both Jaden and Yuma Dueled Chazz and Shark, respectively to snap them out of brainwashing and succeeded. Also both Chazz and Shark used a card that made their Life Points drop to zero so that Jaden and Yuma could win.
How Girag brainwashed multiple students and sent them to attack Yuma in episode 85 is similar how the Yubel-possessed Marcel transformed most students of Duel Academy into Duel Ghouls.
The way that Dr. Faker making an agreement with Vector for the sake of healing his son, Hart Tenjo is very similar to Thelonious Viper desperately helping Yubel who promised to raise his son, Pierce from the dead.
Dumon giving power to Vetrix for getting revenge on Dr. Faker is similar to Yubel giving the power of "Exodia" to Adrian while trapped in the alternate dimension.
In episode 76, a boy is seen in the background that resembles Chazz Princeton.
How Quattro and other people before him being absorbed into the Barian World is similar to how a Duelist who lost a Duel in the Dimension World was "sent to the stars" (killed in the original version).
Yuma getting the Duel Sanctuary Deck and combining it with his own is a lot like how Zane took the "Underworld Deck" and combined it with his. However, Zane forcefully took the Underworld Deck from Chancellor Sheppard after a Duel with him, while Yuma fairly received the Sanctuary Deck from Roku.
Both Yuma and Jaden, at the end of the series, had been through so many Duels where lives and worlds were at stake that they stopped enjoying Dueling towards the end of their respective series.
They both reacquired their love for Dueling during the final Duel of their respective series, dueling with the duelist that started their adventure (Yugi for Jaden, Astral for Yuma).
Like Zane Truesdale's battle with Jesse, Kite died of too much strain on him during the duel with Mizar. However, both were revived.
Unlike's Zane's case, Kite actually defeated Mizar before passing away.
Both protagonist's respective fathers are lost in a different way (Dr. Fudo died after the Zero Reverse incident and Kazuma Tsukumo was trapped in the Astral World). Both fathers also helped the protagonist at their time of need.
Yusei's and Jack's signature cards each have at least one upgraded form, and all of those upgraded forms (not including their /Assault Modes) are Synchro Monsters. Yuma and Shark's upgraded monsters follow a similar principle, but as Xyz Monsters.
When Kite prepares to Xyz Summon Neo Galaxy-Eyes Photon Dragon, he gains power from the Barian World, causing a red aura to glow around his body. Similarly, whenever Jack prepares to Synchro Summon Red Nova Dragon, he utilizes the power of Blazing Soul, causing him to be enveloped in a red flame.
Neo Galaxy-Eyes Photon Dragon and Red Nova Dragon are also similar in that both monsters have effects that allow them to increase their ATK by increments of 500.
The first stage of the Duel Coaster and Girag sending many brainwashed students to get Yuma and Shark's numbers is similar to the Battle Royal that Primo conducted in 106.
Both Vector and Antinomy first appear double agents that pose as their respective series' protagonists friends under aliases (Ray Shadows and Bruno respectively), only to reveal later that they were secretly allied with their respective series antagonists, Vector with the Seven Barian Emperors and Antinomy with Iliaster.
Both Vector and Antinomy have a change of heart after realizing that their respective series' protagonists are their friends, then immediately die leaving them devastated.
The main antagonists of the second season of ZEXAL are the Seven Barian Emperors, similar to the antagonists of the second arc of 5Ds being the seven Dark Signers.
Both groups' members undergo a death and resurrection to become said antagonists.
The way the Heartland City citizens were sacrificed to the Barian World for Don Thousand's ambitions is similar to how residents of Satellite, New Domino City and Grieger's village were sacrificed to summon the "Earthbound Immortals"
Their Number 10X cards are similar to the "Earthbound Immortals". The "Number 10X" cards suppressed the Emperors' true past memories, while the "Earthbound Immortals" gave the Dark Signers the will to live on, even after their death.
Eliphas views Rank-Up as the only way to make the Astral World pure, much like the Accel Synchro Summon is seen as the key to saving humanity.
Don Thousand's Duel against Mizar is similar to Z-one's duel against Aporia. Mizar and Aporia, the antagonists of their respective past arcs, have had a change of heart and confronted the main antagonists of their respective series. Both Duels ended in their losses and deaths. In addition, both Z-one and Don Thousand were able to activate the effects of Trap Cards from somewhere other than the Field or Graveyard (with Z-one activating them from the hand and Don Thousand from the Deck) during their respective duels.
Nash's appearing along with the spirits of his fallen comrades when using the effects of the Over-Hundred Chaos Numbers is a bit similar with Z-one's Duel with Yusei where the latter would recite the summoning chant for each Signer Dragon along with its correspondent owner.
