Sigfried666 said: This discussion made me notice Metroid Fusion seemed to be kinda of an Alternate Storyline. Seems the Metroid story will follow around Metroid Prime storyline. Let's see what Metrid M tells us... (Will at least tell about Samus' past.)
I don't think anyone has said they're alternate story lines. Fusion is the chronological end of the games, if they ever continue it, they'd have to figure out how they'd work the old man in, and how they'd find any more metroids to kill. Prime took place between Metroid and Metroid II, and was written by Americans.
In Other M it turns out that the Baby Metroid had the genetic coding to evolve into a Queen. Samus got DNA from the Baby Metroid and the Omega Metroid in Fusion was cloned from the Baby. It could thus evolve into a Queen eventually. So the Omega could indeed have seen Samus as a rival for the 'throne'.