The game was first announced as "Marvel vs. EA", in reference to how it featured several iconic Marvel characters going up against a group of original characters created by Electronic Arts. In March 2005, the game's final title was revealed, as well as the involvement of comic artist Jae Lee and designer Paul Catling in the creation of EA's original characters, the titular Imperfects. For years, this game and the 2005 promotional tie-in comic "Marvel Nemesis: The Imperfects" were originally their only major appearances in any Marvel property, likely because of the game's poor reception. While it was previously thought that EA owned the rights to the Imperfects since they created them, comic book writer Jonathan Maberry revealed in 2012 that Marvel actually owns the rights to them. Around the same time this was revealed, the Imperfects member Hazmat mistakenly appeared in the first issue of the 2012 comic miniseries "Marvel Universe vs. The Avengers", after the artist on that issue Leandro Fernández mistook Hazmat for another character of the same name from the 2010 comic series "Avengers Academy". The character would later appear as a villain in the 2026 "Venom" comic series, marking the first truly official appearance of characters created for the game in over 20 years.

A sequel was once in the works for the game, though very few screenshots and only one gameplay video were ever released. These materials revealed new playable characters such as The Hulk and The Juggernaut. However, due to poor game sales and the eventual closing of EA and Marvel's partnership in 2008, the game was eventually cancelled.