I agree that the general "avoid combat when moving" bit is a problem, as is the unintelligent resupply kick-in. In my Last set of AI tests, I discovered yet another reason that black holes with damaging warp points are such a problem for the AI. If a human player needs to go through a damaging warp point with a ship, normally he will do it as few times as possible, trying to establish a base on the far side. Not so with the AI. It kept sending ships through, where they would get to the next system (sometimes)only to determine that they needed to be resupplied, so they would turn around and come back through the damaging warp points.
Now that I am done with my AI testing (shameless self-promotion: the Rage Collective is now posted in the mod forum
) I am going to see if I can get a save game to show some of these problems so that I can send it to Malfador. I would recommend that anyone else who sees similar behavior do the same. They have been so willing to fix those things shown to be broken that I suspect this will get taken care of as well, though it may be fairly tricky to fix the resupply issue.