1) Advanced Countermeasures already gives +50% to fighter and missile damage, for all weapons. I stack it religiously on all officers.
2) Big guns can be VERY effective against fighters, AI just uses them wrong. Plasma Cannons (just 2 on Odyssey are enough) or TLs (4 on a Paragon) can clear Astral's complement of fighters almost completely during single approach attempt.
Point is not trying to shoot single fighters as they weave around you, but to concentrate firepower on approaching swarms during their vulnerable approach.
3) Ship hulks create interesting dynamic terrain, the only issue is AI being unable to use it. As of now, this mechanics works purely for player's benefit.