Super Metroid was always going to be a hard act to follow, and during the time of the N64, it turned out to be too hard.
There's been a Metroid game on every one of Nintendo's home consoles, except for one: the N64. The console was passed over in the eight year gap between Super Metroid on the SNES, and Metroid Prime on the GameCube, and according to series co-creator Yoshio Sakamoto that's because Super Metroid was just too good.
Sakamoto said that at the time, he didn't feel like he was the right person to make a 3D Metroid, as he couldn't wrap his head around how to make Samus move with the N64 controller. Instead, he approached another developer - who he couldn't name - to make the game, but unfortunately, the developer turned the offer down, saying that it wasn't confident that it could follow Super Metroid. Sakamoto said that he took that as a compliment to what Nintendo had achieved with Super Metroid, but it meant that Metroid 64 never got off the ground.
Sakamoto said that he still didn't fully understand 3D gaming, but that working alongside Team Ninja on Metroid: Other M had expanded his vocabulary so that he could communicate his ideas to people who did.