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Power up SC/SB gengar?
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Exactly. The defensive breakpoints are much more important for Gengar against Mewtwo. Make sure that damage dealt by confusion drops to 33 and your health points are at least 100. Then you will survive 3 confusions instead of 2 which will boost your damage contribution in terms of more fired shadow balls by survival.
Fortunately the defensive breakpoints are somewhat at the same level as the offensive breakpoints depending on your IVs of course.