Well, challenges have a pilot limit and the ability to exclude each hull class type. This system sort of works to control fleet mixes. But why not give challenge designers even more flexibility?
I propose several different crew types:
A Cruiser would take 1 captain + a command staff of a certain number of officers based on the # of modules and # of crew.
Frigates would take 2-3 officers, again based on the total crew # and the # of modules in the hull.
Fighters take 1 pilot.
Going into the possible strategy game it would be interesting to have these different types of crew to think about and make sure you have enough numbers of as well.