Blackbeard is set up to be one of two possible series-end baddies in One Piece. He IS stronger than Fujitora as the story makes no sense otherwise.
That being said, as of right now, he hasn't had a feat since pre-timeskip where he was loosing to Magellan and we've never seen him fight with the Gura-Gura no Mi.
So by the reasonable rules of vs matches, Fujitora technically wins. But everyone knows he will lose.
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