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Storywise probably tassadar or something before he blew himself up to insta-kill the overmind.
Or I guess the old overmind was the strongest at the time, kerrigan's only powerful because she picked up the scraps of the first war with the protoss homeworlds and terran colonies in ruins and the zerg divided but still strong.
Discussing the most powerful character is ultimately a fruitess endeavor; there is none. Even if Starcraft isn't a perfectly balanced game, every unit is countered by another. There is no superior unit.
Which character is the most powerful is a debate that opens more discussion. If "power" is defined by influence, than Kerrigan is unquestionably the most powerful. She controls the zerg, an army that is poised to wipe out all other known contenders in the galaxy.
But if power is defined by the ability to exert force, it becomes trickier. Kerrigan would still be up there, being a powerful psychic and unstoppable physical force. Zeratul is probably one of the few beings who could contend with her, along with the dark archon Ulrejaz.