I think too many people here, in their rage toward Nintendo, are turning a blind eye to the fact that Nintendo didn't act until after the game had been released. In today's age of information, there is just no way somebody at Nintendo or affiliated with Nintendo did not know about the existence of this project for its nearly decade of development time. I don't care how on the down low it was compared to other fan projects; there were still videos and walkthroughs of AM2R's various demos and whatnot readily available on YouTube during most of that time. The project's existence was not some incredibly well-kept secret.
Of course I have no way to prove this, but sheer common sense leads me to believe that there's just no way Nintendo really did not know about AM2R all this time. If that's the case, I'd say it's very possible - even likely - that they chose not to act until they did to give fans a chance to get ahold of it before they did what they absolutely do have to do and protect the integrity of their IP by shutting it down. (And no, whatever you personally think about Federation Force and whether it's a "real" Metroid title/a worthy celebration of the franchise's 30th anniversary does not matter when it comes to the legal side of how these things work.)
If they knew about AM2R during even a small part of its protracted development period, Nintendo could have chosen to act at any moment - like Square did with Chrono Trigger: Crimson Echoes. They didn't. They let the game see release before they acted in an effort to unofficially satisfy a fanbase they know they aren't currently serving, and IMO they might have left AM2R alone entirely if it wasn't releasing mere days apart from their new in-house Metroid title and casting both their own Metroid title and their own treatment of the series of late in such a negative light. Honestly, Nintendo would have been incredibly stupid not to take action after provocative news headlines about "a single fan doing what Nintendo can't" and "fans celebrating Metroid's 30th anniversary in the way Nintendo won't" and whatnot started making the rounds. This way, at least, they were able to throw the fanbase a bone while doing what they legally have to do by aggressively protecting what they rightfully own.
Or maybe Nintendo really, actually, somehow didn't know about AM2R all this time and issued the takedown order on the first business day they could after learning about it. That's always possible. Unlikely to me, but possible. And even that's the case, they still wouldn't be in the wrong even a little bit - no matter how much it sucks for us fans.
Either way, one key takeaway point is this: no matter how hardcore or devoted a Metroid fan you are, Nintendo owes you nothing. As much as I love Metroid + AM2R and would have loved to see AM2R survive and thrive, Nintendo's acting well within their rights here. A lot of people in this thread do understand that, granted, but this gaming generation's extreme sense of entitlement to anything and everything they want regardless of legal or other factors is also rearing its ugly head here.
If Nintendo did intentionally let AM2R release before doing what they were always going to have to do and take it down - a likely scenario IMO, all things considered - I think that's pretty big of them. Yeah, it would have been awesome and ideal if they didn't take any legal action at all, but it's both very naive and incredibly unrealistic to expect that - especially when AM2R did the exact opposite of flying under the radar upon its release and, instead, drew a ton of attention and was used by many to shed Nintendo in a very unfavorable light.
Anyway, just my two cents!
