Experience is a very important factor when it comes to Capital ships going against bombers or smaller ship in general ( small GB's , fighters etc ) , perhaps the most important one of them all. In the previous mod , even with experience on your side , there was very little you could do against 2-3 bombers , even if they where rookies.
In simple terms , Capital ship pilots had the experience , but lacked the tools needed to serve their role.
Now , however , Capital ships DO have the tools but I'm afraid that most players lack the experience to use them to their ... how should I say ... full potential. When you don't want something to work , it usually wont work. New players , to capital ships , should spend more time testing the weaknesses and strong sides of their ships more.