I still feel justified in assuming Nintendo wouldn't shut the project down. They didnt stop it from being made nor released. Saying they didn't know it existed until it launched is implausible - I made a post here stating Baby Park was the best MK track and Bill Trinen almost immediately tweeted a link to the post in agreement. You bet your ass he and others have read the AM2R thread, and that's just here on GAF.
I think the reason they shut it down, an act which is really unprecedented as far as Nintendo and nonprofit fangames go, is because of this:
They expected it to launch and be a nice little diversion for fans. One dude from Argentina working on a little project is fine - the interest could even work in their favour towards pushing Federation Force sales. Only....that's not what happened. The game launched, and got near unprecedented cover and acclaim around the internet to the point of numerous fans and publications outright stating AM2R is better than anything Nintendo could ever make - and many of them essentially offering it as a direct alternative to Federation Force. The game was getting more positive and thorough coverage than expected to the point of it being viewed as the REAL Metroid game out of the two (sad that it's come to this point).
Nintendo didn't act until they realised the game was so good it was making them look bad. And not only that, making their equivalent Metroid product this month seem a joke.
That's why they did what they did. Otherwise, it would still be up.
even if Nintendo has all the laws in their favor, they created this mess by not making the Metroid game people actually wanted.
if they had actually made a Metroid 2 remake themselves 10 years ago, AM2R wouldn't even exist. this game exists because Nintendo gave the middle finger to fans and now they're mad because people created a way to satisfy their demands themselves. what a bunch of jokers.
i guess the only mistake people made was becoming Nintendo fans.