My understanding of canonical space combat simplified theory is:
Cruisers kill frigates by superior firepower and defenses. However, cruisers’ weapons are heavy and powerful but too slow to target individual fighters. Thus, they employ frigates, to protect from smaller enemies. Frigates’ weapons are perfectly fit to target fighters and their superior firepower and defense let them do so.
In this game, fighters are too fast for most frigate weapons, but even if they weren’t it wouldn’t be very important, as two fighter units can destroy a frigate in a couple of seconds before moving to the next.
Try it. I don’t remember my fighter config right now (I’ll post it later), but it’s a simple combination of “fastest laser” with speed around 2.6. I don’t remember if I managed to put a shield or a second laser.
Anyway, by just deploying all possible fighters (spending almost all pilots), one cheap fighter-killing cruiser and the rest in instances of the cruiser you like most (2 or 3 of them). In a lot of challenges (and most of the single player campaign) the cloud of fighters just goes ahead and clears the screen, leaving some scraps for the cruisers.
I think there should be better antifighter weapons and defenses for frigates. For example:
A - Extremely weak and short ranged lasers but with RoF under 100 and a targetting speed of 4, or so.
B - Some kind of shield module that completely stops most fighter attacks but are useless against other frigates or cruisers.
With that change, the number of allowed pilots could be larger, as players would have to protect somehow their fighters.