I am finding it extrordnarily irritating that fighters and bombers do this. I would not mind if it was a battlecard that was telling them to form up and attack a single target but its not. Because of the annoying focus on a single target attack craft from other divisions are flying across the map to engage a far target instead of attacking the one closest. I just lost three carriers because of this only damaging a single group. (the carriers were captures so not fully or well armed but still.) 

And fighters if not escorting bombers need to be a bit more proactive in defense of a ship, they should be engaging things if they get close, and go after fighters and bombers that are on approach.

What are bombers suposed to counter? Beam weapons? Missles? I've heard they cant perform well against those weps....

The fighter intercept was meant to be resolved with the latest release. Are they ignoring enemy craft altogether or just waiting for them to get really close before intervening?

Regarding what they're meant to counter: big ships. They have the highest DPS vs. carriers if they survive. And anyone who is trying to stay far out of range, as OP notes squadrons can cross over flotillas at will so bombers are ideal for dealing with fleets that tend to stay at long range.

If i have three divisions worth of fighters and bombers, i expect them to fight three other divsions, not focus on a single division on one side of the map.