I gotta agree with the majority of people here.
It's all coming straight from a lawyer acting on behalf of Nintendo's general policies, but Nintendo didn't make the call. Nintendo's producers aren't sitting high up in their offices, sipping red wine, twirling their evil mustaches and seeking out projects to "censor and destroy" like most people seem to be assuming they're doing. Nintendo doesn't even really know this is going on and probably can't even be bothered with it. At least not until it's already happened.
That's why they have the lawyers doing this for them, and occasionally have to make a statement when word gets back to them that people are bitching about something that Nintendo probably didn't even know about until their legal team tells them they simply did their job.
And that's the thing. The lawyers and legal representatives have generalized instructions to be on the look out for unauthorized IP use in illegal projects and to merely inform the makers their their project violates the law and Nintendo's general policies, and remind them of the legal punishments they can face if they don't.
Likewise, DMCA notices (which are pretty much the same thing, just a reminder of the law on this particular issue) are sent to a file hosting service, and the file hosting services are the ones to take the links down, because it's THEIR hosting service, and THEIR policies are also explicitly to cooperate with takedown requests from legal IP holders.
There's also a huge myth that has been perpetuating for a long time that if something "isn't making money", is "non-profit", or "isn't a harm to financial gain" that it's somehow ok, and there's some kind of exception in the copyright law, which there isn't.
Here's how that breaks down....
Companies aren't concerned with direct money being taken from them, they are concerned with their overall brand recognition, and unauthorized connections to works that the rights holders did not commission, license or give an ok to, free or not, hurt that brand identity in the long run.
It can easily be confused for an official product from someone who simply didn't know any better, and even if they did, still dilutes the IP a bit. and it sets a precedent in the public's mind overall.
To put it another way, Nintendo believes that if they wanted this game to exist, they would be the ones to make it. By letting a fanwork blur this line of a high profile, professional work, demeans Nintendo's importance and ability to make and enforce a creative direction on how their trademarks and franchise is being used. And when you have a company that much of it's financial viability is determined by how shareholders or investors view Nintendo's direction, things associated with them like this, factor into how they're seen as well.
THIS is why they run the risk of losing the viability of their trademarks if they let this go. It's entirely possible that a fangame creator can claim everything else BUT the trademarks and become a competitor by essentially taking trademarks without permission. It's seen as an unfair advantage, and can hurt Nintendo's image, hence why they take steps to protect what's theirs.
Adding more to that, It's not just about one fangame here and there, it's basically having to put their foot down and realize if suddenly HUNDREDS, or even DOZENS of fan projects all came out one after another, to make video games directly competing with Nintendo and using their own trademarks and IP against them as leverage to do it, and Nintendo does nothing to stop it, that could severely cripple their company. Even if every single one was free. Brand identity can be eroded and devalued. So, if TONS of fan-projects are not ok, then neither are ANY of the ones that could lead to this, if Nintendo suddenly decided to let water seep through the cracks.
So Nintendo puts a blanket policy in place, hires lawyers and a legal team and tells them to look out for it. It's nothing personal and too many people take it personal and claim it's "censorship". It isn't. It's Nintendo protecting themselves as a business that could be held responsible for damages if they don't. It's also not a "theory", it's a fact. This is literally why DMCA's happen.
People on the internet are too quick to jump to all kinds of inaccurate assumptions and act like Nintendo are a bunch of big mean, bullies who "hate their fans" when A. Nintendo only takes legitimate copyright law into their policy and B. tells that policy to their legal team to take care of it so it never comes across their desk for a single moment. It's not Nintendo's fault the Digital Millennium Copyright Act even exists in the first place. Blaming them makes zero sense.
Likewise, every single instance of these lawyers sending a cease and desist notification to both the creators and the file hosting servers that have the infringing content up on it, not only both the Metroid 2 fangame, and this game have been blown way out of proportion. It's not censorship. It's not personal. It's not even their fault. It's only fair, legitimate, normal, sensible business.
What's more, both of the creators, for Pokemon Uranium and the Metroid 2 Remake have even made statements on their sites and social media as well, urging people not to blame Nintendo and saying THEY respect and abide by their wishes, too. If they aren't mad, no one else should be.
Besides, It already got released and copies are already circulating anyway. Nintendo enforced their legal protective rights and the game is still out there, if you decide to unlawfully track it down anyway, and none of the people that do are are gonna face any punishment for doing so. So even complaining about it is a moot point.
And to add to what others have said... and I realize this has no bearing on anything I just said, I wanted to point it out... I too, looked at it and I also thought Pokemon Uranium kinda looked like crap, anyway. Not like that matters, but there you go. I mean I know they worked hard on it, but if this WAS Nintendo official, i'd think it looks like one of the worst things they'd have done in years.