It only comes into play in campaigns, otherwise all ships are CQ 4, and on average all fleets in them will start with the same spread of crew values. Any perceived advantage is usually balanced out by the fact that a high-CQ ship is typically targeted for destruction pretty quickly, and you're paying for any increase by burning increasing amounts of XP to do so (mostly).
I would like to see the rule from ACTA:B5 back where your starting campaign fleet can swap the crew values of any 2 ships in the fleet, but other than that I don't think it needs messing with.