My brother wants to run an Aliens campaign using the c-system AvP manual, and loved the idea of flaws for the characters, but he's confused about how the advantages/disadvantages should be employed; as how it looks, it can be easily used to make broken characters whith disabilities that doesn't really affect them or have no place in the story. He's thinking in leaving the advantages to choice and make rolls to decide disadvantages at random.

Thoughts or experiences on this ads/disads thing? How is best employed?