So, what exactly happened? Well, apparently, last Thursday, GameJolt got a C&D from Nintendo. GameJolt is a site that hosts fangame projects, and they were ordered to shut down 562 -- count 'em, 562! -- fan games hosted on the site for trademark violation among other things, like profiting off of Nintendo's IP (for those of you wondering about fangames being a labor of love done for free, GameJolt gives you the option for revenue sharing on ads that run as the game loads and on the game pages, with creators looking at a potential cut of 30%, so it's not like Nintendo is wrong in their assertion here).
Now, Nintendo is in their rights here, and in fact, they have a sort of requirement to be hard asses about this. Copyright is actually rather flexible on the part of rights holders, but trademark? If you do not rigidly enforce your trademark, it weakens and you can lose it. And given the sheer amount of name recognition Nintendo's properties have, from Mario to Metroid to Pokemon to Zelda, you can see why they aren't inclined to let it weaken in the slightest. In fact, depending on circumstances, Nintendo can actually be relatively decent about this stuff. For example, an animator decided to make a StarFox fan animated series. Nintendo hit him with a DMCA, because they were making their own StarFox animated series to go out with StarFox Zero. However, Nintendo isn't trying to stop the project. He can still continue with it, he just can't call it StarFox is all. Likewise, one of the games that dodged the massive purge on GameJolt is Escape From Lavender Town, which despite being a Pokemon adventure, doesn't use Pokemon in the title and makes its existence a lot less intricate. (This is part of the reason I'm not sure if I'm ever going to make that Officer Jenny fangame for the Atari.)
Now, I've said it before and I'll say it again -- it's Nintendo's stuff. Not mine, not yours, their's. And if they decide to enforce their rights, for whatever reason or no reason, they can. I'll tell you the truth, everyone should have seen this coming. Nintendo is behind the 8 ball here, and they need the NX to be a smash. They are preparing a massive blitz with any property they have (I'm wondering if we'll see Captain N put in an appearance), and they don't want competition. Just look at Star Trek -- Axanar: people were saying that the preview and trailer looked better than the Star Trek Beyond trailer and people were more excited for it. Paramount would be competing with the fandom it needs to make this work and Alec Peters was acting like a puke (it could have split the fandom over the direction and overall themes of Trek), so out came the ban hammer. Nintendo has a lot of plans, almost none public, so they are keeping the decks clear. And dare I say, Nintendo is actually being pretty lenient here. They could be suing for cash or ruining careers here, but they aren't. They are just stopping everyone from distributing their programs and apps through GameJolt. They can still recover their code. They can still modify it -- Pokemon Uranium is going to keep updating its program for the 1.5 million people who already downloaded it, but they will not be distributing the base game anymore, although you can easily find it on the torrents if you trust that crowd (I don't). So given the absolute ruin Nintendo can create to the fan community, all they are really doing is going, "Me, first." Count your blessings.