The Pokemon Company not saying if Shadow Mewtwo is canon
Shadow Mewtwo was created in close collaboration with the minds behind Pokemon for Pokken Tournament. However, that doesn’t necessarily mean that the creature is a canonical part of the overall universe.
In an interview with Polygon, Pokken Tournament producer Masaaki Hoshino said:
“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.”
“Because everyone really liked Shadow Mewtwo, I have a personal hope that they’ll continue to use it, but it’s not really our decision, unfortunately.”
Tekken producer Katsuhiro Harada, who is also working on Pokken Tournament, weighed in as well:
“For this game, it is kind of a spin-off from the main series. It takes place in this area called the Ferrum Region, which means something like ‘Iron Region,’ playing back into the Tekken connection. So, within the context of this spin-off, [Shadow Mewtwo] is obviously a canonical character. Of course, how The Pokémon Company and Game Freak decide to use the character is up to them, but I think Mr. Hoshino’s passion for the character might inspire them and encourage them to use it!”
Polygon also reached out to The Pokemon Company and asked if Shadow Mewtwo can be considered canon. To that, a representative said “No comment.”