There was supposed to be a chance that the AI would negotiate with you, but a key line controlling that contained a bug and had been commented out. Hopefully that's now corrected, so sometimes you can talk your way out of a fight.
The delivery distance has been changed so the ship now has to get within transporter range of the planet, the starting ship positions have been altered, and the enemy ships on the map should now have an inclination to actually do something during the mission.
Corbo, DOH!, I meant to fix the pirate levels in that prisoner transport mission, but it completely slipped my mind. And I found (I hope) the issue with enemy generation during the salvage mission.
I might also have a surprise in store for the ambush and surprise reversed missions, but still have to test it out a little more first.
dave