You mention how Nintendo was done with 2D games at that point as being a reason no Metroid game came out, but look at what they did with Mario and Zelda games. Funny enough with Castlevania, I imagined a Metroid 64 game being like how Castlevania 64 was for the N64, basically a poor attempt at converting a 2D oriented style of game into a 3D game. I would expect Metroid 64 to have been pretty terrible if it existed.