Give the original text with the standard built in reason for "why" a character has an alternate racial trait. Then give a character specific version as to why which may or may not fit with the "standard" version.
Race(for these examples) Half Orc
1)Skilled: Second- and third-generation half-orcs often favor their human heritage more than their orc heritage. Half-orcs with this trait gain 1 additional skill rank per level. This racial trait replaces darkvision.
Character Specific Version: Character was raised by Sisters of the Golden Eryines (Asmodean Nuns). In order make sure she did not develop the "unfair" advantage of darkvision she was made to sleep in a room with a light spell always lit. She took advantage of this, reading books late into the night. They were her comfort and solace. But never exposed to dark enviroments until adulthood, she never developed the darkvision she would normally have acquired.
2)Sacred Tattoo: Many half-orcs decorate themselves with tattoos, piercings, and ritual scarification, which they consider sacred markings. Half-orcs with this racial trait gain a +1 luck bonus on all saving throws. This racial trait replaces orc ferocity.
Character Specific Version:Same character was whipped by the sisters on a regular basis, in order to "beat the orc" out of her and punish her for infractions, real and made up. To this day her back is filled with scars (like slaves pre civil war). Fortunately, a good spirit was attracted and continues to watch over her.