Temper, the Factions are more like little side quests or random encounters (From a roleplaying analogy), rather than whole additional chunks of AI.
The freedom fighters and marauders spawn ships that attack the AI or BOTH sides, respectively, sometimes to no effect, sometimes being a force to be reckoned with, depending on where and how many spawn.
The Rebel settlements spawn invisibly every few hours on a random planet, and give a countdown. Once the countdown's run out, if the player *doesn't* own the planet by that time, the invisibility's dismissed, and the AI is free to attack. Saving the settlement gives access to some truly evil ships, failing ups the AI progress by a hefty chunk.
There's various active golems too. From the trader, through the devourer which instakills virtually all mobile military ships in a wide radius, to the miner, which destroys whole PLANETS, as if a nuke went off, the Dyson Sphere, etc, etc..