A couple things I think might be useful for challenges:
Balanced Fleet option. A slider that limits both min and max percentage of ships allowed in a challenge. A default of - say - 10% minimum and 50% maximum. So you’d have to have at least 10% each of your fleet as fighters, frigates, and cruisers. The current percentages for each ship type would need to be shown on the deployment screen so you can see how many more (or fewer) ships you’d need to comply with the limits.
Minimum (and perhaps maximum) speed of all craft. Like the ‘engine required’ spatial anomaly, this would more specifically limit the choice of spacecraft that can be used in a challenge. We can already agree to do this when playing a challenge of course, but this would conveniently enforce it.