The problem is that if they split, it's a royal pain in the ass to chase them down with PD ships or other fighters. And it'd be frustrating to see all of your fighters fly off chasing fighters and dogfighting while a squadron of Bombers flies right through and wastes you.
It would shake up a lot of weapon balance, too. Flak would be a lot less useful and Beam PD would be more useful.
Perhaps a compromise...
Fighters/Bombers staying in formation get a small bonus (10%-20%) to their attack. This would give incentive for Bombers and fighters doing Attack Runs to stay in formation. The flipside would be Fighters out of formation would be able to easily flank fighters/bombers stuck in Formation and be less vulnerable to AoE Point Defense. Also, perhaps limiting the "Break and Engage" to Interceptors would give them somewhat of a buff against the currently-dominating Heavy Fighters?
I also believe there needs to be a special option called "Fighter Screen" in the Commands. It would put an Interceptor or Heavy Fighter (Preferring Interceptors if they're available) squadron on a specialized Escort around the targeted ship. While on the specialized escort, they will swarm around their target, covering it from most angles. They'll take off and engage any Fighter or Missile threats that come at their target, but will largely ignore anything bigger than a Frigate.
Kinda like they do in Space Pirates and Zombies. Skip to about 1:30 in to see the Drones in action.
http://www.youtube.com/watch?v=CZeCi8I4zvYThey swarm around like flies, making it easy for them to intercept threats and a pain in the ass to specifically target.