I'm not sure if I'm doing something wrong but I only have your mod pack and my AI is just absurdly bad, like the last 2 posts are talking about.
Ships are just sitting around, taking shields down with a barrage coming at them, going in the middle of a group and aiming a spot with no shield at an enemy ship.
I was doing the first pirate fight in the tutorial and lost my primary ship(I had selected the fast start merc setup, so I'm pretty sure that fight should be over like its nothing)
Have you played the tutorial with your mod active? Not sure if the tutorial could be causing a problem or if its just broken in general.
Something is def wrong though. Hope you get it worked out because this sounds like an amazing mod.
Thanks!