I kid you not, they never explained it.
They have. In the beginning of development, everyone was excited to be making a new Metroid, for the Wii. As development furthered, some things began to become apart to some of the designers. Minor things at first, Samus talked. Slowly, she started talking more, and saying things we would not expect her to. Ridley started taking steroids, nobody said anything because, would you argue with a giant purple space dragon? The changes continues, the story being overly dramatized without needing to be, and having a chain of incredibly dumb side characters. The fps style game-play of Prime which encouraged exploration, slowly changing into a linear action adventure. At one point they took a look and saw what had become of it, and tried to change it back. The money, said no. In shame, they renamed the title, Other M, deeming is so far off from the rest of the franchise, they needed to distinguish it as, The Other Metroid.
Or, that's what I like to believe,