I haven't played SMG2, so I'm only guessing here, but I think that maybe the reason it wasn't nominated in spite of such high ratings is the same reason movies like The Incredibles, The Matrix and The Hangover never get nominated for Best Picture at the Oscars - genre snobbery.
The Academy Awards were set up partly as a way of promoting and rewarding film makers who did work that could make film be taken seriously as an art form. It seems stupid to think that film isn't an art form today, but back when it was just a fledgeling industry, the opinion among serious cultural afficionados was that film was a throwaway form of entertainment - cheap, lurid, flashy thrills for the ignorant masses. They compared film to music and theatre and saw in it a cheap imitation of art, mass-produced and divorced from the artist.
That led the Academy to nominate only the films they felt promoted the medium as a serious art form and be suspicious of spectacle and novelty. The year Citizen Kane released (one of the first films to really experiment with camera/editing techniques - it was like the Matrix of its day), they gave it to a movie nobody remembers these days - How Green was my Valley. Citizen Kane was the better, more influential movie. It just didn't fit with the Academy's vision for the future of film.
The result is that the movies that get nominated for Best Picture are nearly always tragedies, redemption stories, romances, biopics, historical dramas, coming of age stories and war films - Oscar bait, in other words. Comedies, sci-fi and animated films need not apply.
Likewise, the gaming media has a self-important idea of what they want gaming to be. They want it to be taken seriously. They look at something like Mario - a cutesy platformer featuring a moustachioed Italian plumber having adventures in a whimsical magic kingdom and dismiss it immediately because at no point does Mario vow revenge upon the enemies that took his wife, nor is Peach use her sexuality in order to (I dunno) triumph over her enemies, nor does Bowser have a chequered and complicated past marked by tragedy. It's just not gritty. It's just not "mature". In an age wherein the gaming press is obsessed with proving to the world that games are not just for kids, it doesn't fit into the prevailing paradigm.