What kills me is that Nintendo had almost 8 Years to raise a stink about this and instead, their Legal Team waited until 2 days after release to go all Bill Lumbergh on Doc and Metroid Database going "Yeah... we're going to need you to take that down now..."
My current issue with the whole thing is Nintendo giving the statement about the whole "use it or lose it" excuse that says that they need to "protect" their copyright or risk losing claim to it.
Meanwhile, Sonic has countless fan games out there, and I've never heard of Sega going medieval on the makers of those games or the sites hosting them.
Last I heard, they still have their copyright to Sonic.
Now, if I were to wager a guess, the fact the Game was plastered all over YouTube the day of release didn't help as it brought the Completed Game to Nintendo's Legal Team's attention a bit faster.
It probably also didn't help it released very close to Federation Forces' release date since Nintendo probably believes it could cut into the massive profits that will probably never come from FF.
Meanwhile, there's countless fan-games both good and crappy all over the Internet that remain unscathed.
Nintendo has experienced a lot of backlash against its copyright-driven takedowns as of late. Although their removal of NES ROMs and SNES ROMs are far less common nowadays (if they exist at all), the Metroid 2 revamp was something that could cause some confusion regarding who owns what properties of the Metroid name and everything else. In this case, it's not so much bullying or control issues, but rather legit issues regarding ownership.
If a fan-made game doesn't become all that popular (which is usually the case), Nintendo simply isn't going to waste their time on it anymore. It's good to see they're at least starting to get their priorities straight.