I didn't realize troop transports would pirate hunt... I've always had mine in fleets, though - put yours in a fleet and they won't do that.
You'll still have the issue with destroyers though.
Anyone else notice that in the expansion the missile weapons are the absolute best weapon, outclassing everything else? I hope it gets balanced a bit in the next patch, maybe by increasing the speed a bit on the torpedoes and cutting down the damage dropoff at range on the beams a little bit.
The third missile (research level 5) is just better than everything, even the research level 7 stuff. The top tier torpedo weapon has longer range, but at max missile range the damage drops to 18 as opposed to 11 - which would be good except the torpedo travels at a speed of 180, and apparently your ships won't fire another volley until the first one hits. So the actual rate of fire is about once every 4.5 seconds instead of the listed 2, compared to the missile's 2.6 seconds. And if you fired at the max range of 990 it gets far worse. All the torpedoes suffer from this problem.
Then the beams are just way shorter range. The top tier titan beam is range 560, and at that range the damage would be about 6.6, with a fire rate of 1.4. This makes it a little bit better than the missile at that range, but a range advantage of 250 is pretty significant. And comparing it to the beam on the same tech level of the missile is just no contest. The beams still fill a niche role for very high damage at close range, but I rarely find my ships slugging it out point blank. Even with high speed, by the time you close the distance with a missile ship (especially if its flying away from you) you've probably taken too much damage to make it worthwhile.
Not only that, but missiles only have the 1 type - concussion. Ships you build at first tech level of missile are automatically upgraded to the best once you have it researched. All the other weapons are replaced by advanced models at the same tech level as the top tier missile, so once you reach that point you have to retrofit everything.
Oh and an update on my transport problem: It's still obviously there, but starting at a higher tech level (which I kinda hate because I like climbing the tech ladder...) helps the problem a great deal. They still go 5 sectors to deliver 200 units, but at least now they traverse those 5 sectors in half the time and have plenty of fuel left over. I failed to salvage the game I already had going though - I tried adding huge fleets of transport ships with newer hyper drives and such, and it did make my economy get a small boost, but apparently the entire galaxy is so screwed up that my ships are deciding to send packages of luxuries across the other side of the map instead of bringing them to my own colonies so they still aren't reaching their potential. The funny thing is even though my economy is still totally in the dump I'm still at the top of the economy ladder now because everyone else is even worse, even though some of them have a higher population. Even the Teekans with their trade bonuses are slightly behind my economy...