Samus and Link were designed for Marvel Ultimate Alliance

Both Link and Samus were planned for the Wii version of Marvel: Ultimate Alliance, but the idea was canned after Activision decided to put them in without permission (and in the PS2 demo version). Supposedly, Activision told Vicarious Visions (the developer, also a subsidiary of Activision) to include them to "please Nintendo." When the Link and Samus models were eventually shown to Nintendo, Nintendo knew it was the PS2 version (and they were done badly), so they more than likely told Activision to remove the characters immediately or see them in court.