Because I generally don't like to criticize unless I offer a solution, here's an idea. If the CMs decide to keep the scoring-focus on bombers and objects destroyed, how about a rule like this:
Returning fighters on the attacking side are allowed to carry ords on their second sortie only (say after T+60, to avoid it being abused).
1) This would allow for a second strike, which is usually not possible in heavy bomber scenarios.
2) This would encourage combat all the way to end of the frame that is not just furballing on the deck or vulching one side trying to land.
3) The JABO runs would be relevant to scoring and would therefore be opposed (instead of one side just landing after the heavy bomber run and calling it a night).
4) It opens up another interesting planning element for the both attackers and defenders.
5) There would be a much greater "fog of war" during this second phase of the frame.
6) It would also put a higher emphasis on fighters surviving the first raid, instead one side "throwing it's fighters away". As an attacker your reward for re-arming is being able to make a second strike, and as a defender your reward for refueling and relaunching is knowing there will be more targets coming in a second battle.
Bear in mind, this is just a brainstorm, and I haven't thought through all the possible unexpected consequences. Feel free to shoot this idea full of holes.
<S>
Kingpin
