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My wild, out-there theory is that Sylux is the same Metroid-species as whatever the hell Prime originally was. He just took the route of GF experimentation/stealing a GF suit to get to his current form instead of Phazon exposure/stealing Samus's suit.
This would at least explain why Hunters, FF, and 4 still retain the series's name in spite of the original Metroid Prime not appearing/being dead in them.
"does Samus ever stops being alone"
The end of Fusion has her accompanied by Robo-Adam and The Animalz, but as with Star Fox Command and DMC2, I still do not believe Nintendo is all that interested in ever following up that ending.
She has lots of friends in supplemental materials like comic books and stuff, but those are all A. awful and B. not canon.
Other M has Anthony, I guess. Maybe someday we will see him again.
IMO Metroid works best with minimal friendly-NPC presence. Leave the giant cast of friends to Sonic.