Advantages

 Advantages are the offset of flaws, but not all advantages are created equal. The number next to the advantage tells you how many flaw points you need to buy it. You cannot take an advantage and a flaw that are basically opposites. 

Wealthy(1): Your starting wealth is as if you were 1 level higher. 

Separatist(1): You do not have to follow the alignment restrictions of a class. (For example, you could be  LG druid or a Lawful bard or barbarian, or a neutral assassin and you can be a cleric of a god regardless of alignment). You must still abide by any code of conduct or oaths. (So a paladin is pretty much still stuck with LG, and a priest must not act against his deity's interests- including casting evil spells with a good god and vice versa, but a true neutral god could easily have a LG follower without too much issue). This also removes alignment restrictions from certain feats that have them. 

Tool Specialist (1): Choose a specific type of non-magical equipment with a DC (such as a tanglefoot bag, alchemist fire, or a specific kind of poison). When you use that type of equipment, the DC is 10 + half your character level, plus your intelligence modifier instead of the normal DC for that object. 

Old(1): You may play a character of any age category, so you can min-max for those sweet sweet mental stat boosts. You might want to explain why you just started adventuring now. Age stat adjustments are applied first, so they affect the minimum score you can get through dump stat.

Automatic Progression(4): You use the automatic bonus progression alternate rule system. Of course, this means you can't get benefits from magical items. 

Quick Learner(3): Use the "Fast" experience column. You can't have this and slow learner. 

Prestigious(1): You may ignore "dump feat" requirements of prestige classes. Feats whose powers are relevant to the class cannot be avoided, and you must still meet the regular level requirement. Feats like "stealthy", "toughness" or "iron will" are almost universally dump feats. We can talk though them if you're not sure. 

Mover (2): Gain your choice of: A 10' swim speed, or a 10' climb speed. If you gain these speeds through some other means (besides polymorph) they increase by +10. 

Fast(1): Gan your choice of: +10 to your base land speed, or your land speed is not lowered due to encumbrance or armor. You can take this twice to gain both benefits. 

Gestalt (5): You may be gestalt, with the following conditions: We use fractional progression, and you cannot take a prestige class that is basically a combo-class. (We can discuss if you don't know this one). Also, you cannot combine 2 classes that have the same base (such as ninja and rogue, arcanist and wizard, etc.). 

Archetypical(3): You may take a class archetype you qualify for, but keep all the class features you gave up for the archetype. You may not trade those class features away for another archetype.

Trans-Racial(2): Choose another race. You can qualify for feats, traits, prestige classes, etc as if you were that race. (Though you need to meet physical body requirements for some things- for example you can't choose centaur to gain feats that imply a quadruped body).   

Hardy(2): You gain full HP per level instead of average. Animal companions and cohorts and eidolons and such still have average HP. 

Combatant(2): Your BAB progression for your favored class goes up 1 step. (Wizard > Cleric > Fighter). If you already have max BAB for your favored class this won't help you so don't take it. 

Good Save(2): One of your "poor" saves for your favored class becomes a "good save". If your favored class doesn't have poor saves (like monk) then this won't help you- don't take it. 

Energy Resistance(1): Choose one energy type (fire, cold, elec, sonic, positive, negative). You gain resist 5 to that element type, or improve your energy resistance to this type by 5. This can be taken multiple times, each time you can choose a different energy, or increase an existing type by 5. Resistance above 30 becomes immunity. You cannot take this to an energy you have a weakness to.

Complicated(1): You may take a 2nd background. Your backstory must be written in such a way to incorporate both backgrounds. 

Mythic (5): Start as rank 1 mythic. You can gain mythic tiers by completing mythic tasks. 

Teammate(3): Gain a bonus teamwork feat at level 1, and at every level which is a multiple of 5. 

Heroic(3): You can use the hero point system, including spells and magical items and race/class features that augment hero points. 

Trait(1): You can gain either 1 additional trait (beyond the 2 the starting character normally gets), OR you may regain 1 racial trait that you traded away for an alternate racial feature. (But you can't trade it away again). Alternately, if a racial heritage feat exists for your race, you can get that as a bonus feat. 

Multiclass(1): You can choose 1 secondary class as per the Variant Multiclassing listed under Character Advancement. Keep in mind this has a feat cost as you level up. 

Powerful(2): Gain +4 to a single ability score. Treat this as an increase to any racial bonus they get in that ability score. This can be taken up to once per ability score. 

Skill Focused(1): Choose a skill. That skill becomes a class skill. You also gain 1/2 your character level (rounded down) as a bonus to checks using that skill. If you get a class ability that does the same thing (like trapfinding does for disable device) you instead can "Take 12" (instead of 10) at any time, even if distracted, and get the skill unlocks for that skill. 

Classy(1): You can gain EITHER a second favored class OR you can gain a second favored class benefit for your existing favored class (+1 SP or +1 HP). If you are gestalt, you can use this to gain the favored class ability for both classes you are levelling up at once. If a prestige class is chosen as a favored class, this counts as "favored prestige class" for abilities that use that feat as a prerequisite. 

Skilled(1): You gain an additional background skill. You may not have this and unskilled. This can be taken twice. Keep in mind only certain skills are eligible to be background skills. 

Bonus Feat (2): Gain an additional bonus feat that you qualify for at 1st level. This counts as an "insight" feat- as if you wished for it. This can be taken up to 5 times. 

Exotic(1): The character may take Uncommon Races and Hybrid Classes as character options. Occult classes become available as character options, as well as psionic races and classes. You cannot take this and also Basic. 

Charismatic(2): A character treats his level as 2 higher for determining his leadership score (see leadership feat) and for the abilities of a familiar or animal companion. This does not increase an eidolon, reduce the level needed to take the leadership feat, or reduce the level requirement for improved familiars. This does allow a cohort to be at your same level.