I wasn't thrilled about Nintendo's response here. They've known of its existence for the past 10 years- could have hit it with a C&D years ago, but instead waited for it to be released and THEN be a dick about it. While Nintendo does have the right to protect their IP, they're really not protecting it from anything. No harm is being done here, quite the opposite really.
I've played through it in full already, and must say the game is utterly fantastic, enough to rival the other 2D Metroid games. Strongly recommend checking it out, it's the best fangame I've ever seen, and the creator doesn't deserve this treatment for his hard work.