One thing that's bothered me is switching between targets; it's hard to know who you have selected and why. At the risk of offending AnonymousPosterChild further, I added another GUI overlay.
Additionally, NPCs who are leaving the system are now tagged as (Leaving) so you won't try to attack them.
I also added an upgrade item that gives your ship "advanced radar," so now you can see on your radar who is a buddy, who is a star system, and who is trying to kill you.