Instead of a system of points I propose a system of random generation tables.
D100 Roll
Physical Traits
Physical Flaws
Mental Traits
Mental Flaws
Personality Traits
Personality Flaws
Gender Flaws (Refer to the appropriate table based on Gender)
Racial Flaws (Refer to the appropriate table based on Race)
Class Flaws (Refer to the appropriate table based on Class type)

Trait and Flaw Descriptions

Chivalrous Courtesy

Good or Lawful
-4 to attacks vs. any creature you can tell is of the opposite gender.
Code of Arms

Good or Lawful
-4 to attacks vs. an enemy not armed with a melee weapon. Penalty applies to creatures with natural attacks until they use a natural attack on you.
Honorable Challenge

-4 to attacks vs. creatures that have not explicitly challenged your or made an attack against you.
Honor of the Duel

Good or Lawful
Make Will Save (DC=10+your level) to attack a creature in a square threatened by one of its other foes. If successful, you may attack with a -2 penalty.
Mounted Warrior

Ride 1 rank
Suffer a -2 penalty on attack rolls when not riding a mount.
Pride of Arms

Proficiency in all martial weapons
-4 to all attack rolls made with exotic weapons, simple weapons, unarmed strikes and touch attacks.
Solitary Paragon

You gain no benefit from flanking a foe; instead, you suffer a -4 penalty on attacks rolls made against a foe you flank.
Phalanx Warrior

Suffer a -4 penalty on attack rolls when not adjacent to an ally.
Bestial Instinct

Suffer a -2 penalty to hit while using anything other than unarmed strikes or natural weapons.
City Slicker

Survival as a Class skill
-4 penalty to Handle Animal, Knowledge (nature) and Survival checks.

You become shaken while in any space where you are within 10' of a wall/solid surface on 2+ sides, or if the ceiling is less than 10' over your head. Spells and effects that remove fear do not remove this condition.

Automatically fail all Fort saves to overcome the effects of high temperature. Fire-based effects deal +2 fire damage to you.
Forlorn of Men

Become shaken if there is more than one Humanoid within 30' of you, including members of your adventuring party and friends. Spells and effects that remove fear do not remove this condition.
Hot Blooded

Automatically fail all Fort saves to overcome the effects of low temperature. Cold-based effects deal +2 cold damage to you.
Nature Lover

You must succeed at a DC 12 Will save before you can attack any creature with the animal, plant or vermin type, or you lose your action. Animals, plants and vermin may attack you without penalty.
Metal Intolerant

Suffer +1 damage when struck by metal weapons. The natural attacks of inevitable, iron golems and other creatures composed of metal also deal this extra damage.
No Book Larnin'

You are illiterate. You can never learn to read any language, and you suffer a -2 penalty on all Knowledge checks except Knowledge (nature).
Blind Rage

Rage ability
You may not end your rage voluntarily. Once entered, you must rage for the entire duration, and you must attack a creature every round if able. You can charge or move to attack a foe, rather than stay still to attack a friend. If there are no creatures within sight, you must attack the nearest breakable object. DC 15 Will Save 1/round to stop attacking an ally.
Exhausting Rage

Rage ability
When you end your rage, you become exhausted rather than fatigued. For Tireless Rage, you become fatigued after a rage.

Suffer a -2 penalty on saves to resist enchantment and illusion spells and effects. Also suffer a -4 penalty to Sense Motive checks.
Quick-Burning Rage

Rage ability
Your rage only lasts for a number of rounds = your temporary CON modifier.
Slow to Anger

Rage ability
Entering a rage takes a full-round action.

Inability to cast spells
Become frightened whenever you see an item, effect or location that obviously created by magic (whether by spell or other means). Condition lasts until you can no longer see the cause.
Uncontrollable Rage

Rage ability
You cannot enter a rage voluntarily. If something dealt you damage, grappled or immobilized you in the previous round, or you failed a save vs. a spell, you enter a rage involuntarily unless you succeed at a DC 15 Will save (you can choose to fail). You cannot enter a rage more often than you are normally allowed.
Aligned Devotion

Ability to spontaneously cast Cure spells
Your spells of the Healing subschool have reduced effect on those who don't share your alignment (same alignment=full; one step removed=half; two+ steps=no benefit). Cure spells still deal full damage to Undead.
Divine Gestures

Ability to cast divine spells
You suffer spell failure chance when casting divine spells, just as if they were arcane spells.
Domain Devotion

Access to Domains
You choose and have access to only one of your deity's Domains. You may gain prestige Domains from a prestige class as usual.
Living Faith

Ability to turn or rebuke Undead
You lose the ability to turn or rebuke Undead.
Material Devotion

Access to Domains
You may only use spell-trigger items (wands and staffs) that cast spells on your Domain spell lists. Other spell-trigger items fail in your hands (Use Magic Item checks notwithstanding).
Ponderous Spellcaster

Ability to cast spells
Casting times for all your spells increase. Spells with free, swift or immediate casting times require a standard action; spells requiring a standard action take a full-round action. Full-round action spells take two rounds.
Weapon Bound

Devotion to a specific Deity
You lose Proficiency with all weapons except the favored weapon of your Deity. This flaw doesn't grant proficiencfy with that weapon.

Ability to cast spells
Spontaneous noises sometimes arise in your immediate vicinity. You cannot control them, and cannot use them to communicate or distract other creatures. The sounds cease when you are unconscious, petrified, asleep or dead. You suffer a -4 penalty on all Listen and Move Silently checks.

Ability to summon a familiar or animal companion
You lose the ability to summon a familiar or gain an animal companion. You never gain the ability to gain a special companion, no matter what classes you have.
Magical Overload

Ability to cast spells
You must use one of your highest-level spell slots to cast or prepare a spell of a lower level.
Phantom Sparks

Ability to cast spells
Spontaneous bursts of colored light emit from you. You cannot control them, and cannot use them as a light source. The lights cease when you are unconscious, petrified, asleep or dead. You suffer a -4 penalty on all Hide and Spot checks.
Restricted Sorcery

Ability to cast spells without preparation
Choose two schools of magic (other than Divination or Universal). When you select spells to learn, you may not choose spells from these two restricted schools. Also, you may not use Wands or Scrolls that cast spells from these restricted schools.

Wild Empathy
You are vulnerable to the following spells that affect animals, as well as those that affect your own creature type: animal trance, calm animals, charm animal, dominate animal, hide from animals, hold animal. Also, you suffer a -2 penalty to all CHA based skills checks except Disguise, Handle Animal and Use Magic Device. Anyone observing you who has the Wild Empathy ability can recognize this Flaw immediately.
Foe Specialist

Favored Enemy
You suffer a -1 penalty on attack rolls and Bluff, Sense Motive, Spot and Survival checks made against creatures of any kind that aren't one of you favored enemies.

Favored Enemy
You suffer a -4 penalty to your AC and on attack rolls and skill checks whenever you are not engaged in combat with a favored enemy while a favored enemy is close enough that you could engage it.

Suffer a -2 penalty on all attack rolls made with a weapon you have not personally crafted (ammunition doesn't count for bows, crossbows or slings). Also, the Armor Check Penalty increases by 1 for any suit of armor you did not craft.
Terrain Specialist

Track, Wild Empathy
Choose one terrain type (aquatic, city, desert, forest, hills, marsh, mountains or plains) as your home terrain. On all other terrains you suffer a -2 penalty on all Wild Empathy checks and to Search and Survival checks made to track. You may only use your Camouflage and Hide in Plain Sight abilities on your home terrain.
Wild Child

Survival as a class skill
Whenever you are entangled, pinned, or bound, you immediately become panicked. Your fear is alleviated one round after you are free of all bonds. Spells and effects that remove fear do not prevent this effect.

BAB +1
Suffer a -2 penalty to AC during combat until you drop an opponent. Does not apply if the combat is against a single opponent.
Grudge Keeper

If you are damaged in combat, you suffer a -2 penalty to attack rolls, skill checks, saving throws and ability checks until you damage the foe that caused you harm. Penalty does not apply if you cannot discern the source of the damage, and it disappears when the combat ends.

BAB +1
If you move out of melee combat for any reason, you suffer a -2 penalty on all attack rolls, skill checks and saving throws for one hour.
Stubby Fingers

Dwarf, Gnome or Halfling
Suffer a -4 penalty on all attack rolls made with a light or one-handed weapon (natural weapons and unarmed strikes do not count). Also, you suffer a -4 penalty to Disable Device, Open Locks, Sleight of Hand and Use Rope checks.
Elven Pride of Arms

Elven Blood
Suffer a -4 penalty on attack rolls made using a weapon not specifically identified with your Elven heritage (normally Longsword, Rapier or Bow -- Long, Short or Composite). Attacks made while fighting unarmed or with natural weaponry also incur this penalty.

CON <12
Whenver you fail a Fortitude save, you become fatigued, in addition to any other effect you might suffer. This condition lasts until you get 8 hours of complete rest. This flaw only applies once to any given source requiring a Fort save. Failing a Fort save while fatigued makes you exhausted instead.

You become sickened (no saving throw allowed) upon ingestion of any sort of potion for the duration of its effect. Potions of instantaneous duration cause you to be sickened for (minues=potion's caster level). You also suffer a -4 penalty to saves vs. ingested poisons.
Slow Healing

CON <14, must not be Warforged
You do not normally recover hit points or temporary ability damage through natural healing. If you undergo complete bed rest for a full day, you recover 1 hit point or 1 point of temporary ability damage. Also, any conjuration (healing) spell cast on you works at only half its caster level (Example: A Cure Light Wounds cast by a 4th-level Cleric would only heal 1d8+2, not 1d8+4).
Arcane Conundrum

Gnome, CHA 10+
You do not possess the spell-like abilities of other Gnomes (including Speak with Animals). In addition, you lose your racial bonus on saving throws vs. illusions, as well as the +1 bonus to the save DC of any illusion spells you cast.

Suffer a -2 penalty to Listen and Spot checks, and a -2 penalty on Initiative rolls.
Magical Fascination

Suffer a -2 penalty on attack rolls and skill checks when in sight of a visible magical effect with a duration greater than instantaneous (such as dancing lights, spiritual weapon or wall of fire).
Short Attention Span

Your "take 10" skill checks become "take 9," and you may not "take 20" on any skill check. In addition, you suffer a cumulative -2 penalty on all skill checks made to retry an action that you previously failed (-2 to the second attempt, -4 for the third, etc.). All Craft skills are cross-class skills for you, no matter what class you take.

Chaotic alignment
The weight of any gear you carry is considered double for the purposes of determining your load and encumbrance. In addition, any armor check penalties you have are doubled (or tripled for Swim checks).
Half-Blood Outcast

Half-Elf or Half-Orc
Suffer a -2 penalty on all attack rolls, saving throws and skill checks when within sight of an Elf (for Half-Elves) or Orc (for Half-Orcs).

Must make a DC 15 Fort save in order to get a full night's rest. If you are sleeping and are awakened, you must make a DC 15 Fort save to go back to sleep. Failing the save means you are fatigued when you rise in the morning. Modifiers when trying to sleep/rest: Already fatigued +2; exhausted +6; comfortable conditions +4; outdoor conditions -4; sleeping in armor -4. This doesn't affect your ability to prepare spells.

You are not immune to sleep effects and do not gain a racial bonus on saving throws vs. enchantment spells or effects. You are not considered to have elven blood.
Beady Eyes

You lose Darkvision, and have Low-Light Vision (2x) instead. In addition, you suffer a -2 penalty on all Search and Spot checks.

You may not gain the benefit of any kind of Dodge bonuses to your AC. Spells, items and effects that provide a Dodge bonus provide no benefit to you. Also, you cannot use the Withdraw action during combat.
Light Sensitivity

You become dazzled (-1 to attack rolls, Search and Spot checks) in bright sunlight or within the radius of a daylight spell.
Short Temper

Whenever you take damage in combat, make a DC 15 Will save or become enraged. This state confers all the penalties and restrictions of the Rage special ability, with none of the benefits or bonuses. If you have the ability to Rage, the AC penalty stacks while you are enraged (-4 instead of -2). The enraged state lasts for 3+CON bonus rounds, and cannot be ended voluntarily.

Suffer a -2 penalty on Initiaitve checks, and you must spend twice as long performing any skill that requires an action (that is, skill checks that take a standard action require a full-round action; deciphering a page of text takes 2 minutes instead of 1; etc.). Skill checks that don't require an action (such as Concentration or Sense Motive to counter a Bluff) are not affected.

CON <14, must not be Obese
You have half the base weight of a normal character of your race. Height and weight modifers are added normally. You suffer a -4 penalty when making or resisting Bull Rushes, Grapples, Overruns and Trip attempts, and gain no attack bonus when you Charge (though you still suffer the -2 to AC and take double damage from weapons set against Charges you make).

Small size, DEX <14, must not be Lightweight
You have double the base weight of a normal character of your race. Height and weight modifers are added normally. You lose your +1 bonus to AC and attack rolls, and lose your +4 bonus to Hide checks. You must pay double the base cost for armor (but not for magical enhancements); armor you wear weighs 75% the normal amount, not half.

You must make a DC 15 Will save or become shaken whenever a foe engages you in melee. This penalty takes effect as soon as an enemy attacks you while you are within its threatened area. You recover from your fear as soon as you are not within an area threatened by foes.

Rock Sauce, now these are more like it.