1. I always have problem with Vasari cruisers, If you have a level 5 Vorastra smiling in your face with 20 Overseers.. even if I focus fire on them that stupid semigod ship gets level6 no matter what, light frigates are good against them but LOL everything is good against them 
build light frigates in large numbers thats the only thing you can do, but they will die so fast from enemy long range frigates.. and titans, and capital ships, and heavy cruisers are deadly against them too. Antimatter draining capitalship can be good.. IF you have the resources for it..
2. Bombers, uhmm fighters counter them, flak is bad (even in large numbers only scratch Advent bombers as far as I have seen, and other 2 races bombers are much stronger..) BUT, if you face Vasari bomber spam no amount of anti-bomber defenses will save any of your most important ships.. AOE damage is good too, but KOL and Halcyon doesn't do much damage on Vasari bombers, but they are something. Better thing I think to drain carrier antimatter, like moving from grav well to another till the enemy carriers loose all antimatter so they can't regenerate fast the killed bombers and fighters, or use Dunov antimatter drain on carrier fleet. But if your ships are based on antimatter usage and you are not TEC.. the first strategy won't work well, and sometimes you won't be able to lure enemy into several phase jumps but worths a try if nothing else helps 
3. Subverters, try taking them out when you can with anything you have, against AI it worked for me many times, and having your ships in a small area is a really bad idea, or try to move your fleets strength elsewhere, like build a Titan if frigate- and cruiser-fleets are not working well, or have another capital ship. Again light frigates are good against them but they rarely see the last subverter die if you are playing against humans, or an AI kanrak-heavy.
Same as #1, plus as advent the Domina can make you immune... if you have AM.
Domina subjugators are a bad idea I think, they are too late on the tech tree and they should be used on saving capital ships and Titan from being disabled and for repairing important ships, not keeping random frigates or cruisers safe from being disabled.
