Perfect means 'without flaws'. Often, Mary Sues will be perfect. This is a large part of why they are so irritating; it is a character's imperfections that often make them interesting. For example, Neo's perfection of combat means that the majority of fight scenes in second Matrix film are excruciatingly boring, even if they do contain gratuitously large amounts of Hugo Weaving. Therefore, being perfect is more often than not a charge.
It is possibly worth considering, in a philosophical manner, that a diamond that is flawless is almost completely useless. And unlikely to be real. And no one likes a useless synthetic diamond.