Luigi’s Mansion 2 was developed by Next Level Games, an external group to Nintendo. Next Level transferred the GameCube adventure to a handheld format. This second iteration was divided in chapters and was more straightforward than the first title, though. Next Level Games could have developed a Metroid prototype before its work on Luigi’s Mansion 2.
An artist that worked in Next Level Games until 2009 designed some concepts for a Metroid product:
Even Iwata hinted this prototype indirectly when he was asked about his first impression at Next Level Games:
Thanks, Kyoto Report.