No, they need to protect their IP, no matter what. That's the whole crux of the thing. If they perceive this as a derivative work that does not fulfill Fair use, they're more or less obligated to do so in order not to give any idea that they are relinquish any of their rights to any work. Because of cheaters and scammers, companies really need to play it stupidly safe. It may seem stupid and useless, but companies are there to make money.
However, if none of the assets in any sense have been lifted from any of the games, the claim has been done under false pretense and a counter DMCA could be filed. Their claim would need to be rather solid. Seeing how the dev got where he is now, it could be argued that AM2R is a transformative work of some sort. This being a non-commercial venture, I do see them coming top in this, if they choose to go against Nintendo with this. I hope they do and make a successful precedent against Nintendo's habits.
I don't work for Nintendo. I'm here to argue for the sake of arguing.
This isn't abusing as much as it is enacting on their legal obligation, as you put it. Whether or not it hurts the fandom doesn't really register to Nintendo, as long as it doesn't hurt their control over the property. Seeing how Nintendo doesn't really care about certain sections about their fanbase overall, I doubt it's even registering with them. Maybe the faxes would help in this regard.
I honestly couldn't tell you any examples because I don't read fanfiction.
IP protection is not censorship, not even close. Literature has clearly defined rules what is and isn't legal. For example, Bored of the Rings is an example of a parody work that does not infringe copyrights. However, it it was a book about further adventures of Frodo and his gay orgies, and would be sold in a bookstand, the author would get sued for publishing copyrighted material he had no license to.
No defensive as such. Argumentative. The result of companies having to protect what is theirs may have shit consequences. However, these companies live through these products and wanting to keep them as unique as possible only gives them an edge in the market, and taking out possible rights infringing products is what is expected from them.
Because it is a mod. Doom has had a rich modding community for a long damn time now, and rather than trying to shoot them down, Bethesda probably sees mods furthering sales of Doom via Steam. The case is not so with AM2R, as it probably does give Nintendo some free advertisement, it doesn't exactly drive sales of Metroid II like a good mod could drive Doom's.
If I may be blunt, Nintendo doesn't give a damn about Metroid fans. Or most of their fans overall. The executives, designers and producers all do whatever they want in their little projects without any input from the outside. If they were taking sales and consumer feedback into notion, you would see a lot more high-budgeted 2D instead of 3D games. Wii Sports would've seen a new entry on the Wii U, and Sakamoto would have never done Other M. It's less about them fucking with Metroid fans than not really giving a damn what the old school fans want. Federation Force may be a bloody insult to Metroid, but not in Nintendo's eyes. For the developer, whose name escapes me now, seems to consider it as a project to try to make a FPS on a handheld console. Something that Prime: Hunters did pretty well already.
And I enforce the living shit out of this. let your money vote. If a company doesn't do products for you, take your money elsewhere. Buy the competitor's product and showcase that there is a need for more products like this. Customer's voice should be treated like god's command, but seeing staff at Nintendo are some sort of developer rockstars of video game, they don't care until they have to.
Which is exactly why they should cater to all of their fans, not just the hardcore ones. However, as mentioned, they also have that legal obligation to act accordingly.