I can't say about the differences in my empire (I play primarily good) but I CAN say about the AI's. See, here's the difference:
When the Drengin launch an unprovoked war against my peaceful, good civilization to crush my fragile planets and add them to their growing empire, they say something about death furnaces, and then launch their ships.
On the other hand, when the ALTARIANS launch an unprovoked war against my peaceful, good civilization to crush my fragile planets and add them to their growing empire, they say something about having things in common - specifically, again, my planets... and then launch their ships.
See? Big difference, there...
So, is that a good or a bad sign when both the altarians and the drengin decide to crush you in the same game??