It is. That's why the tag line on the back cover of Hermetic Projects is "What are you going to do with all that power?"
Story Flaws are very much what people are saying. They let you tell the SG what sort of stories you want to play, and you get a bonus (VIrtues!) for doing so, so you have a very good reason to look through them and find a style of stories that you would like to play. Very crudely, Story Flaws are for the reactive stories you want to play, and Major Personality Flaws are for the proactive stories you want to play.
They aren't compulsory, because some players won't want to define that sort of thing about their character, and ArM is a game, not a moral discipline. The bonus, however, means that most players will give it some thought, if they aren't strongly opposed to the idea. Making them separate and compulsory would undermine this.