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