Within the game files is an audio clip for an unused special quote when pitting Dormammu against Doctor Strange where the former would say "Doctor Strange, let this be our final battle!". This quote is also in the files of the original release, suggesting Doctor Strange was a scrapped character from the original release that was carried over to Ultimate.
Contributed by Operationgamer17
While Galactus is playable via Galactus Mode, there is evidence that suggests Galactus was going to be playable in Arcade Mode. Within the game’s files are win quotes and voice clips for calling in assists and tagging in other characters, including himself.
Contributed by Operationgamer17
According to Ryota Niitsuma, over 150 female characters were considered for inclusion, but because the team couldn’t come to any agreements, none of them made it in.
Contributed by Operationgamer17
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Rocket Raccoon's victory quote "Never doubt a raccoon." is a direct quote from War of Kings #3, said by Rocket after he incapacitated Gladiator of the Shi'ar Imperial Guard.
Contributed by SilverSupernova
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The giant poster in the dystopian stage "Days of Future Past" is an homage to the cover of The Uncanny X-Men #141 and features a band of characters who appeared in MvC2 but were left out from MvC3. Cyclops, Colossus and Iceman retain their respective places and statuses since they were both in MvC2 roster and the comic cover. Mega Man is shown to be still at large, possibly as a response to the fans craving for him to be playable in the game.
Contributed by Mass Distraction
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In the "Danger Room" stage, Professor X can be seen watching from the background. This resembles his appearance in Cyclops' "Danger Room" stage from X-Men: Children of the Atom.
Contributed by ProtoSnake
There was a discrepancy in Phoenix Wright's level 3 Hyper Combo. When dealing the final blow, he would say "Take this!", while his speech bubble displays "Take that!". This was later fixed in the Heroes and Heralds patch.
Contributed by Makzu
Nemesis was confirmed not to appear in the original Marvel vs. Capcom 3 release due to being deemed "too gruesome", with risk of changing the game's rating. Capcom reworked Nemesis' animations to make him work within a T rated game.
Contributed by shygamerguy
When Iron Man wears his alternate costume "Iron Patriot", his intro line sometimes changes to him muttering "Ugh, I can still smell Norman Osborn's hair gel." This is a reference to the Patriot Suit being designed and used primarily by Osborn during his time as leader of HAMMER.
Contributed by MightyKombat
Although Jill and Sentinel classify Deadpool as a mutant during their pre-fight dialogue, he technically isn't one. His powers are a result of the Weapon X project, rather than his genes, making him a "mutated human" or "mutate", rather than a "mutant".
Contributed by shygamerguy
Firebrand's theme is a remix of the Introduction music from Gargoyle's Quest.
Contributed by shygamerguy
Dante's appearance, as well as his moveset, are based on his portrayal in Devil May Cry 3: Dante's Awakening. The only new moves are Million Dollars, Devil Must Die, Bold Move and Weasel Shot.
Contributed by AkiraTheWarrior
Several characters mention Mundus, the main antagonist of Devil May Cry, before or after fighting one of the characters from that series. Before the battle with Trish, Ghost Rider will say "I eat demons like Mundus for breakfast.". Phoenix (Jean Grey), after defeating Vergil, will say "Perhaps if I'm not too busy, I'll take care of Mundus, too." Dormammu also says to Dante that he should stick to fighting Mundus, implying not only that Dante is not strong enough to defeat him, but that Dormammu is more powerful than Mundus.
Contributed by EFB01
Zero's moveset has at least one move from every game he was playable in from the Mega Man X series.

• The Z-Buster is from Mega Man X3
• Hienkyaku, Ryuenjin, Shippuga, and KÅ«enzan are from Mega Man X4
• Sougenmu and Genmu Zero are from Mega Man X5
• Sentsuizan, and Rekkoha are from Mega Man X6
• Hadangeki is from Mega Man X7
• Raikousen is from Mega Man X8
Contributed by AkiraTheWarrior
The mechanics of C. Viper's moveset are based on her debut in Street Fighter IV: her EX Moves cost meter, and she retains the Focus Attack technique available to all fighters in Street Fighter IV.
Contributed by AkiraTheWarrior
Haggar's Double Lariat costs a small amount of health to use, a nod to how it operated in his original franchise, Final Fight. As a tradeoff, attacks will completely miss him during most of the animation.
Contributed by AkiraTheWarrior
According to Ryota Niitsuma, producer of Ultimate Marvel Vs. Capcom 3, this game was released as a stand-alone disk instead of DLC because the earthquake and tsunami that hit Japan threw off their development schedule.

Niitsuma: After the release of Marvel vs. Capcom 3 there were plans to release DLC. But, as you know, less than a month after the game was released we had the earthquake and tsunami in Japan. That had an impact on everything, and it threw off our whole development schedule. We decided that instead of doing the DLC we could put it all together in one package, add some additional stuff to make it robust and deliver it as a disc.
Contributed by Outofmind23
When Deadpool is first in your party and goes up against Magneto, he'll shout, "HAHAHA! Magneto! Welcome to die!" This is a reference to the 1992 X-Men Arcade game, where Magneto had 2 infamous mistranslated lines, "I am Magneto, master of magnet!", and "Welcome to die!"
Contributed by SOGESNAKE
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If you enter the battle in Deadpool's alternative outfit, "Cablepool", Deadpool will say "And you thought Cable wasn't in this game..." This is a refrence to Cable being in Marvel Vs. Capcom 2, but not returning to Marvel Vs. Capcom 3.
Contributed by SOGESNAKE
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Even though Deadpool is damaged by Ghost Rider's Penance Stare due to gameplay mechanics, in the comics all he saw was a "highlight" reel (e.g. what led to him becoming what he was) and changed Ghost Rider back into Johnny Blaze.
Contributed by SOGESNAKE
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When Deadpool is first in your party and goes up against Spider-Man, he says, "Gonna rough you up like a Broadway musical." This is a reference to the Spider-Man Broadway musical accidents, in which actors portraying Spider-Man from the critically disliked late 2000s musicals often fell from the faulty stunt ropes during a particular scene, resulting in serious injuries and medical attention. After defeating Spider-Man,he will say, "Aw, that was too easy! Maybe it would have helped if you'd turned off the dark!", referencing the musical again.
Contributed by SOGESNAKE
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When you defeat Arthur (Ghost n' Goblin's) as Deadpool, his victory quote will say, "And THAT'S for lulling me into great side-scrolling adventures that were never possible to beat!" This is a reference to how the old NES game, "Ghost n' Goblins" is considered one of the hardest games in history, due to its high level of difficulty and the fact you must play through the game twice in order to achieve the 'good' ending.
Contributed by SOGESNAKE
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When you defeat Dante (Devil May Cry) as Deadpool, he'll say, "Next time, maybe you should let Nero do your fightin' Skippy." This is a reference to Devil May Cry 4, where Nero was the main character for the majority of the game.
Contributed by SOGESNAKE
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Unlike Strider Hiryu and Mega Man characters, Arthur does not have a death animation that mirrors his original death animation, in which he becomes a pile of bones. However, he will become a skeleton in his DLC costume when his powered-up armor shatters.
Contributed by SOGESNAKE
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The Ancient Warrior DLC skin set was supposed to include a new skin for Magneto. This skin was taken from the Marvel event "House of M" where Magneto's daughter the Scarlet Witch changed the entire world. The skin generated controversy because it looked like King Juan Carlos of Spain.
Contributed by Outofmind23
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Magento will reference his son, Quicksilver, when he wins a fight against Dante. "Brash, arrogant, rude, even a white head of hair... You remind me of my son in many ways."
Contributed by Outofmind23
When Wolverine is first in your party and goes up against Frank West (Dead Rising), Wolverine will say "Me and Guys named Frank don't get along so well..." this is a reference to Frank Castle, A.K.A. "The Punisher". Wolverine and The Punisher have a long running distaste toward one another.
Contributed by Outofmind23