Boost torpedoes in some way that they would be dangerous to armored cruisers but not to frigates. Letting fighters drop torpedoes within cruiser shields (and at a survivable speed) is a possible start.
Cruisers should depend on having frigates or laser fighters around to quickly down offensive bombers.
EMP gun is on cruisers. It’s powerful but not very spammable.
Rockets are FOR dealing with frigates; they fire in volleys that wipe the shield out before it can regenerate. If you want frigates to survive, get them to 12+ armor; I can do it and still achieve up to 0.34 speed as Rebels.
Not super long range. Let’s say we made frigate AA have a moderate optimal range of 870. Beam lasers have 770. That means your beam cruisers need to be able to go 100 meters PAST my cruisers on the front line - how often does that happen? Unless you are already steamrolling my fleet, you can’t possibly guarantee that they will.
They still need some DPS. EMP spam won’t stunlock completely, given that the AI is not completely efficient. Give AA missiles low armor/shield penetration and mass cruisers can stand a fighting chance. Of course, you’re right, something else might emerge that is dominant, but that doesn’t necessarily mean that it will. In your example, if I set my priority to cruisers instead of frigates, EMP inefficiency might just be enough to allow me to take out your DPS cruiser support before they do enough damage. Or not - and that could mean that other things could be balanced or buffed, such as EMP shields.
Fighter defense frigates are useful things. Have them hang back behind your cruisers. They will deal with anything that gets in close. If you want to attack with frigates then you need to use speed to your advantage. Speed is life. There is no need for armor at all. Think of them almost like fighters. Fast, cheap, but fragile.