Do you mean in addition to a character's background (human, elf, etc)? If so, I don't see it that unbalancing, so long as you forbid some of the more useful skills from being chosen. What skills that cannot be chosen depend on the type of setting the game is set in. Like restricting the Computers skill in a cyberpunk setting, Disguise and Stealth in an stealth-focused game, or Concentration in a setting with lots of adepts around, etc.
A good way to handle it would be to just give out Talented as a bonus feat, with the two chosen skills must somehow relate to the character's backstory.