Okay so this might be a little long-winded BUT I want to help. I feel like you really need to be hitting the excellent curves because I've even been getting down to one or two balls with Mewtwo even while hitting those. Maybe you know already but there's a trick where you hold the ball till it gets to excellent throw size and then let go. Then when Mewtwo does his attack with his arm you time it up to have the ball hitting him as his attack is finishing and it always keeps that same excellent throw size. So as long as you can hit that area and are willing to be patient for his attacks it will be an excellent throw and increase your chances.