Honestly, the majority of it lies in the story and how it was told. The story was flawed in so many ways, and there wasn't a proper explanation to many things (Why did Adam just shoot Samus? Who was the Deleter?) The story in itself wasn't very fetching to begin with, but the way it was told made is so much worse.
I also have some minor problems other than that, like how each zone felt incredibly boring and basic, and the lacking soundtrack compared to past Metroid titles. Then there's also nitpicky details like how Nightmare looked like a duck and wasn't half as creepy as he used to because of that and his odd fighting style. Plus the random Phantoon cameo at the end made no sense and wasn't necessary.
It did have some good things though, the gameplay wasn't half bad, and I was a big fan of the Metroid Queen coming back. Other than that though, I consider it the second worst title in the series, only ahead of Prime Hunters.