This is kind of a strange question, but I would say that if she is much smarter than you, to the point that you two just can't connect, then you could say that she is too "good", but most people wouldn't say it that way.
Another way that people interpret "too good for him" is that she is too high class, born and raised with money, and he could never hope to earn enough to keep her happy.
Well it depends on the aspect that bothers you. For example: annual income, education level. But then, relationship is NOT a competition, if this girl is with you then she must be attracted by you in your own special way. Don't feel that she is too good for you.
There's a lid for every pot. If she openly loves you for you then believe her when she says it! But if it's just not a good fit, you're just not compatible for each other, doesn't mean one of you is better than the other.