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When the Darkness was extracted from Ven to create Vanitas, Ven was left catatonic. He was able to connect his Heart with Sora's, which allowed him to properly come back, and because of this link, Vanitas' face became that of Sora's.
"And there is a reason that Vanitas looks like Sora. As Sora filled in Ventus’ fractured heart, the fractured part (Vanitas) was affected by Sora and ended up with Sora’s face. So if it had been Riku who had filled in Ventus’ heart, Vanitas would have looked like Riku."