All this copyright nonsense over a free mod is just a waste of resources.

This is what it boils down to, not that these mods are legal. Copyright is basically meant to block anything that could even remotely compete with the work, and give a monopoly over the idea. Doesn’t matter if its a free passion project or a billion dollar company. Thats part of why its so absurd that copyright lasts so long. That said, most don’t want to spend a fortune playing whack-a-mole with their own fans’ free passion projects, unless those passion projects compete with them directly. That might even be why Pixelmon is left up - its seen as too janky to directly compete whereas this mod/game combo is pretty much what fans have been asking GameFreak to make for a decade and as a paid, commercial product at that.