Thor was not included in the game because Storm had similar abilites and was more popular at the time and because he was too powerful, which was seen as hard to adapt.

Shuma-Gorath got in the game by the director of the game, after looking over the character files & picking the character with the most weird, eye-catching appearance — people were used to superhumans from X-Men, so they wanted someone unmistakably inhuman. When the director asked Marvel about adding Shuma-Gorath, they had no idea of the character's existence.