That is the behavior they do now. The fighters/bombers have been way improved. The fighters seem to target other fighters then go after other ships if they run out of enemies. Bombers go after larger ships. And they switch targets smoothly (a vast improvement over Sins1) instead of just standing around thinking about whom to attack next.
Yes I do see that, but I would rather they have static command buttons then having them selected as part of my fleet of ships. Or a separate way to select either ships or fighter/bombers.
Aside from my comment they are much better than in Sins 1 for sure. Just my preferences here, nothing else.