What I would
like to see (which in no way means it's going to get implemented, unless someone else likes the idea)...
1) Beams aren't totally accurate. They randomly fire slightly up, down, left, right, etc. So the only reliable way you'll hit a fighter with an anti-cap beam is at close range. This would be settable on a per-weapon basis.
2) "Get the hell out of the way" AI support. Instead of simply sitting there, the AI reacts to things like beam cannons powering up to fire straight at them. This would also be handy for the Inferno mission.

3) Reprioritization for beam primaries. They're used if a ship is in immediate danger of being destroyed, and hasn't been ordered to attack its target
too strongly.
4) Splash damage realization. The AI understands that if it fires a beam that's five meters wide, and there's a friendly ship inside that five meter diameter, it'll get hit.