For GOTY consideration, I believe many voters keep in mind the sheer quantity of enjoyment they've experienced with a game, something which critics don't really compare between genres when they're scoring for a review.
If you spend 9 hours having fun on Bayonetta 2 then 100 hours having fun on Dragon Age, Smash, Mario Kart, or Destiny, and you take the GOTY question as "which title has brought you the most enjoyment," it's very easy to see why people might vote in that direction.
Besides that, though I can't speak for Bayonetta 2, I thought the characters, story, and universe in Bayonetta 1 were tacky, shallow, and forgettable. I think that's where a lot of the separation occurs down the line, months after people have played it, especially compared to something that sticks in your unconscious like a TLoU or a Dark Souls.
