Wow, and I thought I'm a cynical bastard. I have a firm belief that the vast majority of fan works and especially the biggest projects are made because they love the IP and want to contribute. There are easier ways to seek attention.

People who dedicate hours and months to create artworks or games of their favorite IPs are fans. They don't demand money for their works, they just want to share it with the community and they're certainly not hurting Nintendo in any way.

People need to understand the difference between fair use and plagiarism. Of course I'm not talking about blatant ripoffs in appstores that are merely skins on existing shitty games. Then again unless they're sold for actual money, it's still legal to make them. The bigger Prjects like Pokemon Uran for example are works of love for the IP.

What are we seeing next? Nintendo cracking down on youtube videos for using their footage to review or criticize their games? Oh wait, they're already doing that. Because they're dickheads and think they're above the law and try to strongarm anyone to abide by their rules.

Fair Use is simple but yet complicated at times. Sure I think it applies to making commentary through art and videos (though that's kinda in a gray area like showing movies and tv shows on YouTube), but creating fan made games, especially with no original assets or anything completely differentiate the identity of the project to the original source material...? I'm not sure...

Granted I've not seen Pokémon Uran, but what I've seen from AM2R, I kinda didn't like where it was going. Sure it's the Zero Mission and Fusion into Metroid 2 idea, but using those assets (or very similar assets) owned by Nintendo is kinda crossing that line. Is there such thing as Fair Use of the assets? I wish I knew and I would probably have to read a thousand page document on that. :P

And here's something they said on their website under corporate FAQs.

May I use Nintendo games/music/graphics/web site contents?

We appreciate the interest in Nintendo and in all our video game products. To us, it represents a great sign of success and recognition of the Nintendo brand. 

"Nintendo" is a registered trademark of Nintendo of America Inc. Nintendo owns extensive intellectual property rights in all of its products, including video game systems, game titles, characters, game software, graphics, artwork, and screen shots. Nintendo also retains rights in content on Nintendo's web sites, including articles, artwork, screen shots and other files. Trademarks and copyrights for third-party games and characters are owned by the companies that market or license those products. 

While we are grateful for all the requests for permission to use Nintendo properties, we are not able to grant such requests. We receive thousands of requests and we do not have adequate staffing to review them all. Therefore, our general policy is to decline requests for permission for the use of Nintendo properties. 

Although we are not able to grant permission, use of Nintendo's properties without formal permission by Nintendo may still be allowed under the relevant laws of the particular jurisdiction involved. Thus, we encourage you to seek your own legal counsel if you have any questions about whether your particular proposed use is permitted without Nintendo's authorization. Nintendo cannot provide legal advice.

https://www.nintendo.com/corp/faq.jsp#graphics

So take that for what you will. It sounds like a simple answer for businesses with IPs such as Nintendo but I'm not sure since I haven't had a chance to compare.

tl;dr Nintendo can do no wrong.

That seems to be the basic jist of the OP.

Nintendo has every right to take actions against fanmade games, but it's always a matter of HOW you go about doing things, not that you actually do it. Take AM2R, where Nintendo took action right when the game was finished, not during the years prior when some levels were available and everyone knew of its existence. It seem kind as a shitty behaviour and I would much rather see them take actions but praise all these extremely talented developers who contribute to the Nintendo brand.

And so? M and AO rating are sperated by 1 year of age. If countries weren't up in arms about the AO rating. This sex mini game, would of been kept in the main game. My argument stands. The moment people say "kids", you can't argue. We have a stripper dance mini game, in GTA V. Are you going to say V is acceptable to kids?

It's not a grey area. As long as you're doing transformative work, on the content. It's a grey area, if you're doing those react videos. And showing the whole video etc. I've personally dealt with the automated system on YT, in my review videos. I filed counter claims, and won them. Because I followed fair use, to the letter. Companies will be dicks on YT, regardless. I've had to wait the full month window, for them to drop it.

I'm in the middle of this debate. I wish Nintendo was more lenient and allowed people to make fan games without shutting them down, but they're not in the wrong for doing so either, since they are their IPs and they have to protect them. So they kind of have to do it. Although I don't believe Nintendo doesn't enable their fans. They do so in other was, such as showing off fan art and being active in the youtube community.

I don't think it's as simple as saying "Sega's good for letting their fans make fan games, while Nintendo is evil for shutting them down!" I'm sure there's more to it than just that.

There's also something to note, despite shutting these games down, games like the Metroid Remake and Pokemon Uranium are finished games, so people can still play them. It's is still sort of a win for both sides. The creators of fan games can still show off their games, and Nintendo does what they need to protect their IPs. It's better than a few games that never even got that far...

The creator of AM2R is crying somewhere..

Sega is just an irrelevant company imo if you don't live in SEA or Japan. The fact that they're using Deep Silver instead of themselves to publish Atlus titles in Europe isn't a good PR sign either (that makes them less innocent than Nintendo in my book)

Nintendo is unique in that they have a rather silly number of classic old games that they still make money off of to this day, so it has never surprised me one bit that they like to keep free fanmade alternatives that are often little more than enhanced versions of their own releases off the market. That's entirely reasonable to me... they need to show people that their intellectual property will indeed be protected and by this point everyone should be well aware that it will be.

They generally go after anything that is similar to a product they themselves plan on releasing, which makes plenty of sense. Just recently, for example, they initially shutdown the Kickstarter for that Nintendo art/coffee book until they'd laid out some guidelines and rules, and just a few weeks later we learn Nintendo is also releasing their own very similar book.

It really appears that whenever they have plans to release anything, be it an old game, new game, or some other product, they look around to make sure someone else isn't basically ripping them off and selling/giving away something similar.

I hope Nintendo take down all fan games. Most of these fan initiatives come from the West and the last thing I'm interested in is Americans touching Japanese classics.