During development, the game used designs based off Grant Morrison's New X-Men run and a non-cel-shaded look. including a New X-Men-inspired look for Colossus that was specifically designed for the game. This was later changed to being based upon the Ultimate verisons of the X-Men and adding cel shading to make them "pop" more, so that the characters would be more easily readable during gameplay. Regardless, personality traits of the characters resemble their mainline 616 counterparts, and alternative costumes based on the X-Men classic appearances are available.

Kitty Pryde was briefly considered as a playable character, but due to her phasing ability possibly breaking the level design, she was scrapped and replaced with Magma. Kitty Pryde later appeared as an NPC in X-Men Legends II: Rise of Apocalypse.

Before having Magma as the audience surrogate, Raven Software originally wanted the player to create their own X-Men, which would have allowed the player to have custom powers. However, Marvel turned down this idea.