Articles with headlines like this really bug me, it’s all assumed reasons rather than even the tiniest about of journalism.
The prototype was made single handedly by Metroid Prime 2 and 3 programmer Paul Tozour. However, when footage was shown to Kensuke Tanabe, Metroid Prime series producer at Nintendo, he wasn’t keen, which Tozour put down to unfamiliarity with Portal.
So sure, maybe they “didn’t get it”, maybe your prototype sucked? There’s about three people I trust to make a portal game any fun at all, and it basically requires all of them. Portal without the humour? Portal without the not too difficult not too easy puzzles? Portal without the sandboxy engine?
I get this with the argument against game demos. Sales go down when you release a demo ahead of the game? Your game is bad!