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Traits are chosen at character creation, and have pros and cons. Perks are chosen at certain level up intervals, and are pure bonus Swift learner should be a good reference: http://fallout.wikia.com/wiki/Swift_Learner

Perks never had negative sides in FO1 and FO2, only traits did.. "Fast learner" is an exact copy of its older counterpart, except that it gives 10% in FO3 and only 5% in the original