I think the reason the graphics are so simple is that probably most of the game is zoomed out side scrolling 2D. However, at times they zoom in for dramatic cut-scenes (very likely) and continue using the same models.
Also, there may be any number of odd sections involving full 3D (for boss fights or those forward scrolling action sequences), but once these areas are played out, they would likely not be accessible any longer (instead it would open a new path or you would trot through the same area in side scrolling 2D after the action sequence or boss is done). This may well be, essentially, a 2D metroid with some 3D boss fights and 3D action sequences to punctuate the 2D exploration.
If so then WIN WIN WIN