Much of the story is actually told through the gameplay. Adding gameplay such as sneaking around corners, hacking computers, and tricking guards are key to a fun and interesting level. It's much easier to create a mission by thinking in smaller terms. Don't try to build a map of San Francisco. Instead, pick a smaller area and make it more detailed and active.
Activity leads to more creative choices for the player.
Gameplay and replay value is enhanced when you let the player decide how to complete a mission. Provide different weapons and different routes to certain locations. Choice is always good. Test it, tweak it, and play it. Smith gives a good example of how to make the game logical.