Why is there no Metroid on Nintendo 64?
Because its director could not see Samus on that controller, and the studio Nintendo asked instead said no.
Between Super Metroid (1994) and the double launch of 2002, eight years pass without a new Metroid. The Nintendo 64 came and went inside that silence. The gap was not neglect so much as a genuine design problem nobody at Nintendo could solve to their own satisfaction.
THE GAP
1994 to 2002Sakamoto’s objection
Yoshio Sakamoto has said plainly that he could not imagine how the Nintendo 64 controller could be used to move Samus. The man who would have had to direct the game did not believe in its controls.
The refusal
Nintendo offered the project outside the house. The unidentified company that was asked declined, unconvinced it could build a worthy successor to Super Metroid. The assignment stayed unclaimed.
Samus, elsewhere
The character did not vanish: she is a fighter in Super Smash Bros. (1999), and her gunship anchors a table in the Virtual Boy’s Galactic Pinball (1995). The series, though, has no N64 chapter, the only Nintendo home console of its era it skipped.