The thing that I think they improved the most in metroid prime 2, was the graphics and the adventure. In the first Metroid Prime the levels where all base on elements, like a normal video game: Magmoor caverns=fire level, Phendrana drifts=ice level, Phazon mines=underground level, Tallon overworld=land level, Chozo ruins=ruins level.
But in this one it's not just like a video game, there's adventuring between two worlds. One the dark version of the other and the other is the light version.