Let me preface this by saying, I get why you would want to get rid of the old point buy rules as it is possible to create very unbalanced characters with it.
With that said, player's should be able to get SOMETHING for voluntarily giving up that vital of a stat in the game.
Yes, it can be fun to role play a character with a major flaw, but this is a role playing game so unless there is some mechanical advantage, you could do just what the game is designed to help facilitate and ROLE PLAY being sickly or brutish without taking the mechanical penalties.
If you are playing an Elf, and you take an extra flaw to CON, your CON could be as low as 6, which is a -2 mod. If that elf is a wizard or sorcerer, at first level, they will only have 10 HP.
That means that there are a total of 11 common martial melee weapons that can drop them from full HP to 0 HP on the damage dice alone. If you calculate in the fact that many fighters and barbarians will have a +4 STR mod to damage at first level, almost every common martial melee weapon could drop that poor elven sorcerer from full HP to 0 on the first hit.
If that is the case, then why on Golarion are they even adventurers? That is, unless they are exceptionally gifted in some other area beyond other sorcerers.
So, here is my proposal to maintain balance while still giving a mechanical bonus for voluntary flaws:
First of all, keep this as an optional rule only used at GM discretion.
Second, limit the taking of optional flaws to a single set of ability adjustments that takes place at the same time they gain boosts for taking the flaws. As they all happen at the same time, each flaw and boost must be placed in a different ability score.
In this way, a character can take, at most, three flaws, each dropping a different ability score by 2, and gain, at most, three boosts, which add 2 to most ability scores but could add 1 to an existing 18 and make it a 19, but still must apply to 3 different ability scores.