First off, there's no "improving the base AI"... it's not available to "improve". Alex was kind enough to write a method whereby we could write our own AIs from the ground up, but that's it. So yes, this was written completely from scratch, which was a lot of work
Second off, the emphasis on the Player's ship was pretty intentional, but it's pretty apparent that:
A. The weighting on the player over other enemies is a bit too heavy.
B. The weighting of the AI causing it to stay out of combat in general might be a bit too heavy.
C. There are lots of little issues remaining to get worked on, like smarter missile use, etc., that make the enemy AI a bit weaker than I'd like.
I haven't felt like any of that was game-breaking, per se; I can see how it might make things easier if you have a lot of ships, but frankly, by the time you have a big fleet and lots of Officers, the game's not hard at all vs. Vanilla's AI, either.
Fixing both of these things is fairly straightforward, but requires a lot of playtesting. I've been (slowly) working on this here, but I haven't released anything in public to update it for a while, until I'm a little happier with it