Combat missions work best when their battles serve a purpose - preserving a trade route, for example, or conquering a foreign city to stop invasions of your own city, or to open a new source of raw materials. Use the Editor's randomization capabilities to vary the invasion point, timing and troop strength and keep players on their toes, unless you have an overriding reason to schedule a particular invasion force at a particular point. Terrain can make for an interesting dimension in combat missions. Players who enjoy combat generally hate monument building, so if you include monuments at all in combat missions, keep them fairly small. Ratings and population requirements should be modest, too, since the real purpose of a combat mission is survival.
Political missions are the toughest to create and the most fun to play.
Your design should reward consistency or loyalty and punish opportunism. Political missions usually include economic incentives and military punishments. You must clue the player up front about what's going on. In Pharaoh, we used the mission briefings for this. Players who didn't pay attention to that briefing had a lot of trouble with the civil war missions.