learn how to take advantage of the battle system. once you figure out a strategy that works, try to stick to it. just don't get caught with no dodge and your enemy on the red -- you'll surely get a barrage to the face.
my current strategy? kiting the enemy. my current ships' ranges are around 20k, well beyond the ship ranges of my current enemies in chapter 4 (i figure they're around 15k to 17k), so even if its only the primary weapons that are hitting them, i'm pretty much safe from counter attacks as long as i can stay out of range. it also helps me to have Ian as my first officer. Mr. Precise pumps up accuracy, so even if i fire around the fringe of my weapon's range, most of them land. of course, i can always duke it out with all weapons in range, but i've got smaller ships that hurt when i take a 5-ship volley. so i whittle them down, then maybe duke it out for some serious volleys.
and it pays to grind for better ships. it's a pain, but it'll get you through some tough spots to have better ships than to rely on combat skills. Elgava's boss fights will hurt you seriously. i mean it. XD