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I like the idea of the PvP missions even though it doesn't sound like they will be fully implemented at release. I would really like to have missions where PC villains have the mission of kidnapping someone or robbing something while the PC heroes try to foil the scheme - or heroes guarding an event while villains try to disrupt the event (like steal a hero-guarded nuke or knock out a hero-protected mayor's speech).
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Could add a whole new level of difficulty to respec missions. Maybe something like a villian respec team trying to destroy the reactor and the hero respec team trying to protect it. Only one side could win.