I tend to allow my players a try's at rolling, and if they are horrendous they can pick using the assignation method.
One of the problems generally with the Startrek system is that the species aren't ballanced against one another.. they are built using a variable number of points (for their base template).. So you can't really have completelly fair and ballanced characters. Only a couple of my players have tried to munchkinise their characters, most opt for just playing.. what they want too, and let the skills lie where they are suited too .. and they tended to do much better because they had a much broader base of skills to draw from and not just uber one trick pony