Ultron's more "dog-like" head design featured in the game, which deviates from artist John Buscema's original design from the comics, appears to be based off of a promotional image featuring a prototype of the Ultron action figure produced by Toybiz for the Marvel Legends "Legendary Riders" series of toys. The final version of the action figure would instead feature a more humanoid head.

Originally, the Mattie Franklin iteration of Spider-Woman was planned to appear as one of Spider-Woman's costumes, with even concept art being made of her. In the final game, she was replaced by Mayday Parker (Spider-Girl).

Throughout the game, various characters are skeptical of Black Widow's intentions. Daredevil however defends her and is certain she isn't a traitor, mentioning that he fought beside her and were both romantically involved in the past. This serves as a reference to the Daredevil comic book series (later titled Daredevil and the Black Widow), where both characters co-starred together between issues #81 through #124 in the early 1970s.