The Number of the Beast (Greek: Ἀριθμὸς τοῦ θηρίου, Arithmos tou Thēriou) is a term in the Book of Revelation, of the New Testament, that is associated with the Beast of Revelation in chapter 13.1 In most manuscripts of the New Testament and in English translations of the Bible, the number of the beast is 666. In critical editions of the Greek text, such as the Novum Testamentum Graece, it is noted that 616 is a variant.
Basically the number 666 is considered evil due to things in the Bible and Vivillon's cute and innocent appearance is considered ironic as it would be expected that the evil numbered Pokemon was evil looking.
Source + I'm a hexakosioihexekontahexaphobe