If you don't use flaws in your game, and if you've turned on any book that adds its own traits, like "Character Traits Web Enhancement" (which is turned on by default), the APG, Ultimate Campaign, or any of the adventure paths, then you can avoid the Feats/Flaws issue by turning off the "Use Traits & Flaws" option, since the "Use Traits" part of that is redundant if you have any of those other options turned on.