Apparently it was the best showing of stereoscopic 3D of any medium and that along with great art direction is why they got the award. According to a comment by one of the editors. Basically even tho technically both BF3 and Metro: LL were better, style and 3D trumps that.
I guess it's a pity that EA didn't partner with Nvidia to show some 3D BF3 gameplay @ 120hz, they probably would have won if they did.
Oh and keep in mind the fact that a Wii game won last year beating KZ3
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