I agree, I don't care for the way flaws work currently. I have not been able to find any way of being able to effect either the severity or the number of flaws in a new ship. To me this seems to be moving the game in the direction of a simulation rather than a game. A game is supposed to fun, while a simulation is supposed to simulate something regardless of whether that is fun. If this is supposed to be a game then I would at least like some ability to control the number and severity of the flaws a new ship receives.
In the current state I simply ignore the flaws since the AI has them just the same as I do, so our ships are effected roughly equally.