In the case of AM2R and the 500+ gamejolt fangames, I'd say Nintendo was completely justified. Give me a single reason anyone would buy Metroid II for 3 bucks on the eshop if they could just play AM2R, a game that not only is free, but is overall filled with more content. And gamejolt lets you earn money if people play your fangame, AKA you can make money off of Mario, Zelda and Pokemon without actually owning any of the IPs, not to mention there's always a possibility people would think "Why would I buy the official games if I could play all these fangames for free?". I WILL agree that No Mario Sky and Pokemon Uranium aren't justified, though the Uranium devs claimed that Nintendo didn't tell them to stop
Just wanted to say...
Technically, they are legally justified in any takedown notice.
So that's not the issue with AM2R.
The issue with AM2R (and Uranium since it was a similar case), was that it was literally in development for a decade.
Nintendo had AAAAAAALLLLL of this time to issue a takedown notice.
The game had numerous demos, soundtrack previews, and the like, so it's not like it was under the radar or something.
And I'm pretty sure the VC port of Metroid II was out for a while before the game fully released too.
But Nintendo only decided to issue that takedown notice when the game was OUT. Finished. After a decade of work. After all of the blood, sweat, and tears had already been poured into it.
That's just plain
rude.
It's especially jarring when Nintendo just hasn't been doing well at all lately, in terms of delivering games their consumers want. Lately, it's felt like they are just going out of their way to do what people never asked for (SMtxFE except it's really Otaku J-Pop Stars: The Video Game), if not things people have been vocal about not wanting (a sequel to Sticker Star). Not to mention even situations where it feels like they explicitly put less effort into it a game than previous installments in that same series (Mario Tennis: Ultra Smash). Of course passion projects like AM2R will pop up when a company does that. In Metroid's case, the company doesn't do **** with the franchise for years, the last game was panned and legit ruined the reputation of one of their beloved characters, and then they decide to make a chibi-fied spin-off starring faceless soldiers. They are literally not handling this situation elegantly at all.
If they were smart, they would have left AM2R alone. Even better, they could give it an official blessing and promote it a bit (like what Capcom did with Mega Man X Street Fighter, which worked out well). But no, they did the WORST possible thing, and decided to try and gimp the project at the most HORRIBLE time (both when the project was just finished after a decade of work, AND during what now feels like an unceremonious 30th Anniversary for the Metroid franchise).
Metroid II on the VC also isn't much of a defense. Nobody was buying it. Nobody in 2016 wants to play a bog standard port of a game from an extremely dated console, when better options from that same franchise exist on the Wii U eShop. Or when there is an upcoming spiritual successor to Metroid (Axiom Verge) launching on Wii U. Not to mention, Nintendo REALLY did nothing to advertise Metroid II's existence on the eShop. Like, most people didn't even know until AM2R came out.
There's really no defense for what they did, it was a boneheaded move from every possible angle. And the fact that it is becoming a trend with them lately, makes it even worse. I wouldn't be surprised if they take a stand against Smash modding or something at this rate.
They exercised their legal right, but that alone as a reason to do something is juvenile. I would be legally within my rights/not breaking any laws if I went to London and started singing "Get Out Ye Black and Tans", but it would still be an incredibly tactless thing to do that could potentially make people want nothing to do with me. Nintendo as a company thrives on people wanting something to do with them, so the last thing they need to be doing (especially now, in such a critical time for them) is actively making people pissed off with them.