I ran a bunch of trials on a couple of different savegames last night and never did come to a good understanding of how the targeting works - in one case a group of cruisers left a few bombers for last on every run, and in one case prioritized killing a newly-warped-in tank and two fighters over five bombers that had been sitting within range for several minutes.
Are you talking about how your ships are targeting, or how the AI targets your ships? The AI uses a lot of more complex rules and fuzzy logic for what it does, so it's very hard to predict what it is going to do.
For your ships, mostly it tries to do the maximum damage to enemy ships while also minimizing the damage possible from enemy ships. This may make cruisers target on ships that are non-ideal targets to hit more out of fear of the damage those ships can do to the cruisers than anything else. It may be leaning a bit too much in that direction, I will have to look at that.
But, you're right about different playstyles - if I really want to watch the missile-vulnerable ships die in a glorious firestorm then that's my style and I'm totally willing to pause/queue to get it accomplished. (Plus, it suits my antique computer well - once the fleets get big, the only time I can really meaningfully interact with a battle is on pause, so double win!)
Hopefully some of the performance improvements in K will help. It should be around a 40% bump in speed in big battles. At least, that's what I was measuring in my test games.
I think it speaks very well of the game design and balance that people really do play it in so many different ways and enjoy it.
Speaking of playing and enjoying... time to go do both!
Thanks! I've been really happy to see how many different playstyles are out there, too.