This is old news by now. It's already been known since the beginning of the week and widely covered on a
whole bunch of gaming news sites.
There's no argument to be had over whether Nintendo had the right to do it (obviously they do), the main question has been why Nintendo would only now bother going after a tool they've avoided for a whole decade and the only real answers seem to be that either they have something like a Pokemon-maker in the works (maybe some Pokemon-themed DLC for the upcoming MV Trinity release on Switch) or they never treated it as a serious problem until the release of Pokemon Uranium lit up their detector like a nuclear launch.
I've seen all the common argument about "well, they packaged ripped assets and had Pokemon in the title so it's their fault" which utterly ignores the fact that certain other wikis and fansites hosting huge quantities of ripped graphics with "Pokemon" in their titles have still been allowed to stay open. Clearly it wasn't just the rips or the use of the Pokemon name alone that had it targeted but because it had code to make a game packaged together with it, even if that code itself wasn't ripped or infringing.
Generalizing this as simply "Nintendo protecting their IP" is overly dismissive of the fact that this wasn't just protecting their IP in general but Nintendo stopping people from making fangames. Specifically -fangames-, not just hosting rips and sprites of official assets.
Yes, it well may be a stance they have always adopted since the beginning of time, but there's no point in pretending it's anything less specific.
If they're going to invest the hundreds of hours to make something like this happen, then they need to just scrub the Pokemon name off of it and move on.
This also disregards that the whole point of Pokemon Essentials being a way to make Pokemon fangames. Not a Digimon fangame, not a Yokai Watch fangame, not your generic monster-catching Fakemon fangame but
Pokemon fangames.
You can deride the people who want to make Pokemon fangames as "lazy" or "copycats" or "morally wrong" or misguided all you like, but at the end of the day, most of those fangame makers (at least the ones using Essentials - the ones behind paid phone games like Pocket Master are a different story) are mainly doing it because they are fans of Pokemon and for little other reason.
There's no point in pretending the kit was ever made for anything broader than to indulge fans of Pokemon who wanted to make fangames of the series, so suggesting they could've gone generic is fairly laughable and perhaps almost insulting to those Pokemon fans.
And no, before anybody tries to jump down my throat, I'm not one of them. I don't make Pokemon fangames. I enjoy myself a bit of Pokemon, but I have never used Pokemon Essentials to make anything in my life nor did I even realize it was even still around prior to Uranium getting released.