Is there any way to either
1) increase the effectiveness of the ai
2) add the species from the vanilla version to the mod
I set 2-3 ai at max settings against me but it just isnt the same, I'm not sure whats wrong but the ai dont seem to vibe w the mod xP
The Vanilla ships don't stand a chance against the modded ships. Generally damage output is far higher from the modded ships. Modded ships also have a very different shield and armor characteristics and shield mitigation is used in the tech tree to toughen newer ship designs as the tech tree is unlocked.
As to the AI, it has many known and several suspected behaviors. Basically its dumb. At higher levels of toughness the AI is given additional resources as compared to PC players. I'm not sure how the AI achieves "aggressiveness" but the code implies the AI is given goals and works to achieve those goals. An example would be destroy N planet modules or X ships or Z type of ships within some time frame. It's also good to know there are several AI. Strike craft for example have their own behaviors.
Probably not the answers you were looking for but did that help?