Really cool. Thanks for sharing this. I would have been even more blown away if it was running on actual N64 hardware, but it's not too far off. The textures and the Samus model just looks a bit too sharp to me for N64 graphics, although it might be a bit more believable towards to end of the generation when larger cart sizes and Expansion Pak support was more common.
I agree that the 3rd person concept would have been what was used for an N64 Metroid game. FPS games really weren't able to successfully achieve platforming during the N64 era. Most of the best FPS's just didn't allow jumping at all and the games that did (Turok, Shadows of the Empire) the platforming was extremely awkward. Metroid Prime was actually a pioneer in this regard since Retro figured out that it was best to allow the character to actually be able to walk a meter or two past the edge of a cliff before falling off. This concept essentially made first person platformers viable and it was ahead of its time in 2002. I am just not sure if developers would have been able to discover this sweet-spot back during the N64 era, they probably would have just stuck with a 3rd person view at that point in time.
It looks like a lot of work went into this. Given that NoA Legal is likely to issue a Cease & Desist and shut this whole thing down any day now I have to really tip my hat to this person who put this much work into something that it likely not to have much of a future. It's an interesting vision of what could have been.