Yeah, I have to babysit a bit to kill specific targets, but the reason they default to that I think is because it is hugely effective in a standup battle.
Look at the weapon effectiveness grid: fighters do 4 times the damage to bombers that they do to almost everything else (double the damage they do to other fighters), and because almost everything else tends to miss strikecraft are one of the very few things that are very effective against other strikecraft.
Basically, if it is going to be a long carrier fight, your fighters wipe out their bombers quickly - rendering their carriers toothless and saving your ships. In a medium or short fight though (for example, if they are fleeing) wiping out their strikecraft doesn't matter too much as they will just rebuild them, and won't have time to kill your ships anyway.
In those cases, I babysit my fighters and focus on a few key ships I want to kill before they get away:
- planet bombers are easily killed by fighters (double damage), pretty expensive and dangerous to my economy
- capital ships of decent level are a tough nut worth cracking if I can do it (jump negators, decent firepower).
- I sometimes focus on repair ships if I suspect I'll be fighting their fleet again soon, to make sure I get kills quickly
- long range ships are also double damagable by fighters and dangerous to my fleet, but the AI would probably target them next anyway, so I usually just let the AI handle it from here.
