Well, power is relative when it can be beaten by Gengar, but the new boss patched into arcade versions of the Pokémon fighting game is definitely a darker version of Mewtwo.
Here's a video of the new Mewtwo versus Gengar grabbed from NicoNico by YouTube's TrackerTDGaming.
Over at NeoGAF there is some speculation that this new form of Mewtwo could be from the rumoured combined version of Pokémon X & Y, Pokémon Z. Others suggest this Dark Mewtwo is a creation exclusive to Pokkén Tournament and won't bleed over into the proper Pokémon titles.
More will become clear as we get closer to Pokkén Tournament's early 2016 international Wii U release.