Yarlen has come out and stated that AI will not be open to modding. However, he did say that they would like suggestions for improvements. Even suggested a new thread for it.
So I figured I might as well getting it going.
1. Better capital ship building selection.
2. Better building placement. Especially Starbases and other defenses.
3. Better tactical abilities such as handling enemy starbases like going around instead of suiciding on them.
4. Better autocasting
5. Better ability targeting. No 100 Utility Cruisers focused on one ship.
6. Better prioritizing of targets. Siege Craft vs others. Trade ships vs others. etc.
7. Better AI expansion.
8. Sliders? Maybe?
9. Better scout pathing. Avoid double backing and pirate bases.
10. More commands to give to AI
a. Colonize planet
11. Control over whether or not AI's can build super weapons.
12. Better researching
Thoughts? Other recommendations?