I've brought this up before, and I don't know if it's been brought up again, but I remembered this idea. Why not have some fighter beams (perhaps, in a campaign, they could be considered new tech) that track and sweep with a fighter/bomber without bothering with the three stationary fires. For the actual method of the beam tracking, I was thinking you could have tbl tags comparable to the tags that control the tracking/correction time of the missile targeting reticle. That way, any Joe with the tbl's can change how hard it is to dodge the beams.
In the end, the effect would remind you of phasers in ST.
Kind of as a counterpoint, perhaps to put things back into more balance, a command (in FRED, and in the ships.tbl to indicate the default) to prevent beams (at least anti-fighter beams) from penetrating the shields, and just damaging the shields instead. I suppose the balance could be worked out as we go...
A third idea I just had might be handy for the latest in stealth/covert craft... Perhaps a type of countermeasure could be added. This countermeasure, instead of just fooling missiles, would produce a sensor ghost of the original craft for a few seconds. Because it wouldn't be a visual decoy (I'm kinda repeating myself here), it would be handy only for fighters with low visual profiles, and fighters in nebulas. Just to make it cooler (and to give more automatic use, even if minimal, to AWACS), it might be coded so that the decoy is ineffective within a certain range of enemy AWACS.
Just some ideas:)