There are plenty of flaws they could give her without changing her backstory or family or context:

- Stubborn and hard-headed
- Prejudiced
- Believes her way of doing things is "the best way"
- Overbearing
- Too honest, terrible liar
- Kind of a killjoy
- Too focused on tradition
- Overcompensates for any mistake (that she actually acknowledges as her mistake)

are all flaws that are totally believable for her as she is now.

Besides, every group of characters benefits from a "straight man", and Twilight is not an acceptable substitute for that role, since she is the one that is meant to learn the most and her breaking under pressure and neurotic outbursts makes her a bad candidate for it anyways.

When you're best pony but still underappreciated…