I've been having trouble countering plasma siege starships in my current 9/9 game. Specifically one of the AIs is a kite flier/starship fanatic. On defense I can use needler turrets, but when I'm attacking an enemy planet full of starships my only mobile ship with a bonus against artillery is the bomber. And surprise, bombers are vulnerable to engine damage. Since I'm playing on ultra low caps the amount of ships that get their engines completely disabled per plasma shot is far too much to bear, and bombers aren't a reasonable method of fighting them as a result. Even if the bombers are able to destroy them after getting their engines blown out, the fact that bombers also are good against many starships in general means I really need to keep them alive (and mobile) when attacking such a planet.
My problem is also magnified by the fact that the enemy starships auto-kite, as my fleetships become worthless if the enemies move out of range after destroying my engines. Guess I didn't think things through when I signed up for that AI combo.