As I experienced, especially in my own character concepts, how much picked talents and flaws can mess up a character or better put the game balance, a random distribution seems to be a wise choice. On the other hand, why not allow them to chooe one of the talents, maybe the minor one. I always resented gettting a magic talent when playing a non-magic user and the other way round. Let the players have at least some say in this. Otherwise you could really end up with completely useless talents.
The other idea would be to talk to players about what they would like to have and then see how this can be achieved, even if not in full maybe to some extent, an extent that is helping but not unbalancing the game.