According to former Senior Vice-President of Capcom USA Christian Svensson, the reason why Cyclops, a mainstain of the series, is not in this game is because the team felt they already had too many X-Men characters and didn't want to add another one.

Gene from God Hand and Mega Man were in the final pool for possible playable characters, but neither of them made the final cut, because the team wanted to put other characters from the same category instead.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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".

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.

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.

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 Kūenzan 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

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.

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.

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.

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!"

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.