The point isn't a GM not using them against the players. The point is players picking flaws with little to not actual effect, because it impacts something they can't really be any worse at to begin with (Wizards are awful in melee no matter what, another -2 isn't going to actually hurt him much; if the Barbarian is climbing, he can't fight at range anyways). It's best, as BH said, to just ban them entirely, because either they're free power with no real penalty, or you go out of your way to 'punish' the player and end up causing bad blood for no gain except a sense of superiority.
Lunar, dead link. You should probably just give a URL link to the strip in question (and I think I know which one it is).