I think this is a problem with any sequel to a game that features multiple biomes as locations. Metroid Prime had a lot of distinct locations: a volcano, an icy ruins, abandoned villages and temples, a crashed ship/underwater section, etc. So if when making a sequel, you have to consider if reusing these types of areas will make it feel too much like the original.
I do agree that the environment of Metroid Prime 2 is kind of bland, but there are at least some distinct parts I can remember, like the swampier area, or the dessert. I prefer that to every game being a march through the same cookie cutter areas every time.