With all due respect to Jiggs players, Mewtwo dominates this matchup. Shadow King hit the nail on the head - but don't forget his up and down tilts as well, both of which are lightning fast and have insane coverage.
Jiggs can't Wall of Pain Mewtwo very easily simply because Mewtwo has too much range and speed in his recovery options.
Remember also you don't need FULL Shadow Balls all the time. Baby Shadow Balls are a tremendous nuisance for characters with poor approach options.
Not to mention the fact that up throw kills at INSANELY low percents.
The main thing to worry about are YOLO Rests in the air and on the ground. But as far as I know she has no actual guaranteed Rest setups against Mewtwo, so just try to avoid option select situations and you'll be fine.
I hope that was helpful. Best of luck!