It sucks. I agree. I just discovered the playthrough of it that the AH crew was doing and wanted to play it myself, being a fan of both pokemon and minecraft, only to find that everything's been discontinued.
To all those who are angry at nintendo, the pokemon company, and gamefreak:
First, it should be noted that nintendo, the pokemon company, and gamefreak are not all the same thing. Gamefreak only makes the video games and don't have much say in pokemon as a whole outside of what they create. Meanwhile Nintendo is the huge company that rules over the actual first party stuff like mario and zelda, and similarly likely had little to do with it, at least not directly. The Pokemon Company are the ones who sent the C&D, and in spite of everything you think:
They had little to no choice.
If you head on over to the official pokemon website, scroll all the way down and click the "legal info" link in the bottom right, you'll get a neat little paragraph that says, among other things, "Pokémon, Pokémon character names, Nintendo 3DS, Nintendo DS, Wii, Wii U, and Wiiware are trademarks of Nintendo"
The key word there being "trademark". Trademarks have some weird rules that make them different from copyrights in that the more lenient you are with your trademark the more likely you are to lose it entirely. This is what leads to all those really stupid lawsuits like when bethesda tried to sue over the Scrolls games having Scrolls in their title since it could potentially be maybe kinda confused with the Elder Scrolls series. Check out this video for more info:
And continuing on with the pokemon company's legal info, the entire second paragraph deals with "derivative works based on the copyrighted property trademarks, service marks, trade names and other proprietary property", which is how they define "fan art", which is the closest thing pixelmon could be compared to if you wanted to protect it. And of course everything's in legalese, but basically the rest of the paragraph says "The pokemon company owns your fan art and can do whatever they want with it", and your rights to your fan art are pretty much restricted to "a personal, noncommercial home use", which this mod is clearly far beyond
Sign the petition if you wish, nothing bad will happen if you do, but at the same time The Pokemon Company isn't in much of a position to revoke their decision