With all this controversy in stem cell research and whatnot, would it be possible for certain technological advancements in Spore to be protested by your people? In my opinion, this would make getting some advancements harder than just getting the required amount of money. Some mini-games could be tied in to the actual debates or you could choose to finance the project behind the public's back (with a risk, of course). I don't have any idea about a good mission that would turn the people's opinion over, but ideas are welcome. Some especially hard missions would be made for the genetic engineering tech, of course. It would just make getting that ultimate technology so much sweeter.
Another thing that bothered me about the Civ series (I didn't play Civ 4 so excuse me if this was included) was the peace agreements. They were always limited to just stopping the fighting. In this game, it would be a nice touch to add more flexible armistices. For example, you limit the size of their opposing person's army, make sure they don't manufacture weapons, etc.. This is way closer to real world.