Yeah, this really does seem to be taken deliberately out of context on kotaku's part. From the sounds of it, he basically wanted something more akin to Metroid/Super Metroid in presentation and control, but Team Ninja wanted 3D. The end result was a mixing of the two.
What concerns me is that could mean what I have feared, that the 3D elements will be awkwardly shoehorned into what should have been a branching paths/2D experience.