I think Smash is worthy, but its mostly an iterative and content-based improvement of a well-established formula. Otherwise, yes Nintendo got hosed. If there is a bias, I think its to "mature" games and then Nintendo games get pigeon-holed into "Family" category. Its kinda the way Oscar movies treat all non-drama type of movies, like the rest are just niche and not serious.
I will say that I feel like Nintendo hit more home runs this year than anybody, but they didn't have a grand slam like BOTW. But, I think the rest of the GOTY nominees are in the same boat. I don't think there is a clear frontrunner or a choice that 75%+ are going to agree with and respect even if it isn't their personal GOTY. We don't have a clear cut choice that most everyone would respect like BOTW and GoW in recent years.