Pharaoh's missions can be divided into Economic, Combat, Political, Terrain and Freeform types. While you can and should blur these lines, always define what blend of core concepts you're going to follow, and make sure that your mission design always advances your guiding principle. It's possible to craft an economic mission whose pressures are driven by scripted events, but this is exceedingly hard to balance. You're more likely to succeed by concentrating on resource availability and trade opportunities - the structure of your city and its place in the world. Economic missions are well suited for monument construction, as well as for high Prosperity and Culture requirements.
Combat missions are probably the easiest to make.
Give players a couple of years of gametime to get an economy running, and start throwing invasions at them. Start with small forces and work up to large ones. To keep non-combat pressure on your players, pay attention to the price and availability of copper and wood. 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.