The shadow ball one.
Iv's are kinda blown out of proportion for legendaries/legacy moves, moves >>> IV's (aside from rare instances on glass cannons, which Mewtwo is definitely not) The lucky 96% is not useful for much aside from being a more expensive eevee evolution thats outclassed by a number of other pokemon, legendary and non (only completely outclassed as an ice attracter by mamoswine), a slower gym clearer that machamp but less potion efficient than MM metagross ith similar dps. or with psychic beign the top machamp counter and nothing else.
Unless you're aim's to only do solo tier 3's and not legendary raids Power the shadow ball one up, niantic kinda screwed mewtwo by removing shadow ball.