Well, first of all, your plan should note that Charlotte's Future Shock hits all foes.
Secondly, Manaphy is a legendary with stats exactly like Shaymin. Charlotte's Future Shock is "moderate damage" after all (50% paralysis chance to all foes aside). I doubt it would go down to two attacks. I would personally use Shaymin instead of Togekiss to first attack Manaphy, which would double the power of Discharge and Future Shock.
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