The Civilization, Dungeon Keeper, and Settlers series are all hybrid games, each one a cross between a CMS and a war game. In addition to their economic challenges, all feature exploration and conflict challenges. The military aspect of The Settlers is quite simple, as it must be, because the economic aspect is exceedingly complex. Dungeon Keeper begins each scenario with construction and management of a dungeon complete with semiautonomous denizens. In the later stages of the scenario, the player takes his army of creatures into battle, and the construction activities are finished. Control in Dungeon Keeper is a curious hybrid of direct and indirect control in that creatures have a distinct behavior model but obey orders as long as they're happy. (Unhappy creatures disobey or even desert.) However, Dungeon Keeper retains its economic challenges throughout: It's one of the very few games in which the troops have to be paid, fed, and given a place to sleep.
If you're going to design a hybrid game, design the economic simulation first (unless it's really simple) and then add the other elements afterward. Because the other aspects of the game usually depend on the underlying economy, a mistake in the economic design can easily ruin the rest of the game. For example, a war game that includes an economy for weapons production might lose all its strategic challenge if the player can produce weapons too quickly. The player will exploit his economic strength and overwhelm the opposition with sheer numbers rather than strategic skill.