The flaws that weren't
Many Mary-Sue’s have flaws that don’t really count as flaws, and still make them absolutely perfect. Here are some of them.
Being too pretty or too good at everything
There’s nothing bad about being pretty or good at a lot of things, it’s just what people say when they try to defend their Mary-Sue’s so they don’t have to fix them.
This does not mean all stubbornness, only when the characters are only stubborn until somebody explains it do them, then they change their minds.
Rage or temper problems
Not all characters with rage issues are Mary-Sue’s. A Mary-Sue with rage issues will never attack or even snap at any important character (such as the love interest). The Mary-Sue would also only attack characters that fully deserve it.
This is sometimes used to make her seem more innocent. Funny how it goes away as soon as the intended love interest/popular friends start talking to her.
Mary-Sue’s will claim to hate their powers, often saying, “I just want to be normal.” Even when she has no weakness and is loved.
Some good flaws to give your character
Being a hypocrite
Aggression towards others
Being a control freak
Always making a victim of oneself
There are hundreds of other perfectly good character flaws out there, these are just some of the better ones I’ve found.