People are not like exam scores or diamonds, there is no such thing as a 'perfect' human. For that matter, since flaws are only meaningful in contrast to perfection and 'human perfection' is meaningless, there is also no such thing as a 'flawed' human. Which is to say, even thinking about people in terms of 'perfect versus flawed' is kind of silly.
I prefer to think in terms of vices and virtues: habits of mind and personality traits that tend to promote moral or immoral action. Overcoming (a) vice is thus confronting and changing a part of yourself that makes you do bad things (or fail to do good things). Overcoming (a) vice does not make you a 'perfect' human being, just one that will probably behave more morally.
I should also differentiate vices and virtues from 'quirks' -- vices and virtues are part of what makes a character unique and interesting to read, but they aren't the whole picture. For example, Monk (from the TV show) has quirks that make him amusing to watch, but which are not either virtues or vices. We would not want him to 'overcome' his quirks* -- they make him fun to watch, and give color to his personality.
* Except when his quirks become vice-like, such as when his fear of dirt prevents him from chasing a suspect down into a sewer. And even then we don't really want him to permanently overcome his phobias -- just, with much agonizing, do what is necessary despite them.