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.

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.

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.

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.

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.

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.

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.

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.