One of the things I enjoyed in Gal Civs II from a role-playing standpoint was political parties. I really liked them, and I would like to see greater emphasis placed on internal political rivalries (more parties, more fighting for votes, etc.)
Another thing is governments. I liked the idea of governments, but I felt they were too straight-forward (Federation = swimming in money). I hope to see more government types based on preference, each offering different bonuses (like political parties) and have it affect how it affects you diplomatically and internally:
ex. Democracy, Republic, Theocracy, Kingdom/Empire, Oligarchy, Military Dictatorship, Totalitarian, Hegemony, etc. Each should have their own bonuses and draw-backs (Military Dictatorship gets Hit point and weapons bonuses but take hits happiness; while Democracy gets happiness bonuses and some economic bonuses but a bit more instability with politics). The way I wrote it makes it seem more complicated than it really is.
Just throwing out some ideas/things I would like to see there.