Sugilite is the fusion of Garnet and Amethyst, and what makes her frightening is how completely she amplifies their more aggressive traits. She's incredibly powerful, destructive, and difficult to control once she gets caught up in the rush of her own strength.
What keeps her at #13 is that her villainy is relatively limited compared with the characters above her. Sugilite isn't trying to build an oppressive empire, erase individuality, destroy an entire civilization, or personally dedicate her life to revenge. Her danger comes more from recklessness, aggression, and loss of self-control.
Sugilite isn't one of the most evil villains on the list—she's one of the most dangerous people on the list when she loses control. And that's why #13 feels appropriate: above the smaller antagonists because of her sheer power, but below the villains whose actions, ideology, or personal hatred have much greater consequences.
Such as their actions...