In-game, Mewtwo would definitely win. It's got better Speed stat, heavier defenses, stronger offensives, and more HP. It has access to plenty of moves as well, and after only just one use of Calm Mind, it would become nearly impossible to stop. Whenever its health gets low, it could always restore itself instantly with Recover. Mewtwo might be super-effective against Darkai (since it's a dark-type while Mewtwo is psychic), but still—it would definitely be the victor. In anime, though, I'm not exactly sure who'd win. xD They would be equally as strong probably, so I'm guessing it'd be a tie?