Nintendo never did compare or sell MP as a Halo killer. It was from the net that the idea spawned from. That so called need for a Halo killer was redundant. Games better than Halo appeared years ago and continued to appear during that generation. Unfortunately they were all on PC.
If nothing else, MP help branch out and expand what a FPS shooter could be. It had been a long time since anything as immersive as Deus Ex or System Shock had came out. Neither games were "Vanilla" FPS. MP went further by breaking out of the weapon staples of melee, pistols, shotgun, automatic, explosives, "Exotic". But there is no mistaking it, MP is a FPS, it's not traditional, it moves away from the standard so far it almost forms it's own genre.
If Gunpei Yokoi was still alive, I would imagine Metroid would have made the leap to 3D at the same time as Mario64, but considering that 3D was new back then, Metroid might have define, at least initially what a console FPS is if they made it an FPS. However it would have more likely would have been a 3rd person affair.
The question I ask of Ghost is, what are the "Roots" of Metroid? If it is 2D for you, then you should already be satisfied with the handheld offerings. The exploration, the energy tanks? The shoot to open doors? The different guns? Most of the staple 2D elements from Super Metroid are found within MP and are expanded for 3D. Some were removed due to gameplay/control limitations, but where was the outcry from the disappearance of the fire flower from Mario 64?
Because MP was released one generation late, it will continued to be mislabeled and poorly looked upon critically. Was MP even possible back then when a FPS wasn't done right on a console until GoldenEye and for the Playstation, MOH. If a 3rd person Metroid was released, what would have stopped it from becoming Castlevania 64? Maybe they knew they couldn't get it to work to the level they expected of themselves. Basic R&D weren't ready or had not been done, things like the lock on function in LOZ

OT. The so called dream team was only so big.
I hope a lot of these background questions would be answered one day, not just for this game, but many others.