I was really a fan of the x1 Caesans, I really like how they were very similar to the "real" grey aliens, I think it adds a nice bridge between the game's setting and real life while also raising some interesting implications (maybe the conspiracy nuts were right in the Xenonauts universe?)
I also like having at least one or two clean and "professional" looking common enemies, like the x1 Caesans, Harridans, and Wraiths. I think it's a nice reminder that the enemy, while capable of making beastly, terroristic forces, is also dominant in its ability to field large numbers of organized, professional, highly skilled forces. It makes me feel like the aliens really are dominant in all spheres, and that the only way to really beat them is to get creative, carefully choose engagement situations, and figure out how to use the aliens' advantages against them.
In terms of mechanics, I think enabling more advanced behavior when different tiers of officers are on the map would be cool. Maybe some aliens are working together to press your position from two sides, and running a guy around back to disable their officer makes them less cohesive (for instance, maybe when the officer is present, some units provide covering fire and others advance, and when he's gone they act more independently).