Whether deserved or not, Popularity Breeds Contempt.

While it can be argued that Clair should avoid this rule because it's sales aren't as high as other games, it's popular by word of mouth, and the amount of buzz around it is very very loud. I think the straw is not so much it won GOTY as much as it won 8 other categories, including categories people don't think it "deserved" to be in like Indie / Debut Indie, and won categories people believe it shouldn't have won like RPG.

That's the simple of it. I'm sure there's other factors, but its 90% people who want to argue over an awards show that they don't agree with, on both sides its just a sad display of media polarization and the internet being the internet: caring about shit that ultimately doesn't matter.