Samus Aran doesn't appear in the cartoon series because storyboard artist and writer, Jeffrey Scott "never heard of her," despite the character's archenemy being the cartoon show's main villain.
Samus Aran is a beautiful space hunter from Videoland. Her primary adversary is Mother Brain. She uses a starship called Hunter IV to travel between worlds and competes with Princess Lana for Kevin's affections. Samus is impressed by Kevin's skills and believes he would be better off as a space hunter.
Samus was likely written into the comic to fill the gap left by the various third-party characters who were turned down to appear in the comic series.