I consider carefully all flaws characters take it has to be something that will
a) Fit the Campaign
b) Be a disadvantage
I limit allergies to uncommon substances to one per character unless it is obvious to opponents. I also guarantee the allergy will come up at several oppertunities.
Incompetence I require be in a skill which the player could reasonably use so obscure skills are unlikely to be allowed.

But making sure that the players characters are properly balanced with each other and fit the campaign is part of the GM's job. All game systems have problems and all points design systems can be exploited. In the words of Hero system ' A disadvantage which is not a Disadvantage is worth 0 points'