At one point in time, both Link from The Legend of Zelda series and Samus Aran from the Metroid series were playable characters. The reason why both of them were removed is unknown, but it is speculated that it is due to Nintendo being shown the character in a PlayStation 2 version of the game, and that they weren't happy with their characters appearing on a competitor's console.

Arin Hanson, also known by his YouTuber alias Egoraptor, provided the voice for Dr. Bruce Banner during the development of Marvel: Ultimate Alliance after winning a contest held by Activision. Hanson described the experience recording Banner's lines as "humiliating" as it was the first time he had to work in a professional recording booth let alone for a AAA video game, and believed it was a bad performance. Hanson initially claimed in 2013 that his voice was used in the PlayStation Portable and Nintendo DS versions of the game, but a DS version does not exist and he is not credited in the PSP version. In a later email correspondence with a user from the Lost Media Wiki, he stated he recorded his voice after Activision informed him that it would be used in select versions of the game, those being the Wii, PSP and PlayStation 3 versions. Since this was also a local contest, Activision assumed that all auditions were coming from Los Angeles and in the surrounding areas. Hanson got a "congratulations" email and was invited to Los Angeles for recording, but he was unavailable at the time. His recordings ultimately went unused in favor of another voice actor due to time constraints from Hanson only getting a chance to record late in development. However, his unused recordings would end up being added in the 2016 re-release of the game.

Moon Knight and Colossus are not on the roster of playable characters in the PlayStation 2, Xbox, and PlayStation Portable version, but they can still be accessed on these versions by using an exploit.