The other character I've voted for is Sorceress Ultimecia. She had no motivation for her deeds - she just did them. Between possessing Matron and causing international war to releasing the most powerful sorceress of the time, all in hopes of accomplishing a world where only she can exist ... there's not much else but pure evil for the sheer sake of it, right there.
Well Ultimacia hated the SeeDs, all of them, mainly because she knew they were destined to destroy her. Due to that, Ultimacia slaughtered as many SeeDs as she could, as we can see when entering her castle, bodies scattered all over the place, they were White SeeDs.
Her motivation was to rule through all times, to have past, present and future merged together to spread chaos and ruin through ages.