Shadow Mewtwo is the final boss of Pokken Tournament, but The Pokemon Company isn’t confirming or denying whether he’ll appear in other Pokemon games and media from here on out.
According to Bandai Namco producer Masaaki Hoshino, his team worked in conjunction with The Pokemon Company to create the character for Pokken Tournament.
When we were originally coming up with the design, we worked very closely with The Pokémon Company and Game Freak to make sure everything was right. What happened was, we at Bandai Namco had the idea of making a really cool dark-colored Mewtwo, so we had one of our designers take a crack at it and then presented that to The Pokémon Company and Game Freak. They all thought it looked really cool, so then we worked together to brush it up.
The Pokemon Company was asked if Shadow Mewtwo will become canon to the rest of the Pokemon series, since he appears in Pokken Tournament as a canon character, but the company refused to comment on the matter.