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Base Mewtwo: Replace Pressure with Berserk and remove its hidden ability.
Mewtwo Y: Replace Insomnia with Psychic Surge.
Mewtwo X: Replace Steadfast with Moxie.
For Mewtwo Y, take 35 of the 40 points put into Attack, put 15 of them into Speed, and 20 of them back into Defense, giving it base 115 Attack, 90 Defense and 155 Speed.
Add the following moves to Mewtwos move pool:
>Earth Power
>Moonblast
>Close Combat
>Swords Dance
>Knock Off