Zoning and Land Use
What type of city you are building will have a large impact on how you build it. You should ask yourself whether you want a small city that is comprised of mostly homes and small commercial buildings, or a large city with tall buildings containing primarily commercial and industrial organizations. While this may sound like a lot of trouble to go through for a LEGO city, choosing the type of city you want will impact the entire design, and can be the difference between a poorly constructed city and one that is well-constructed and thought out.
Road Placement
Think about what type of city you want to emulate when you are laying out the roads in your LEGO city. Modern, urban cities often have wide, straight streets laid out in a grid pattern (think of New York or Manhattan). Smaller, more rural cities are more likely to have narrow, winding streets, and may even have dirt or gravel roads in some areas. Also consider whether you want to place large freeways near your city, or have them looping around the outskirts of your city. Depending on how many LEGO bricks you have to work with, you can design overpasses through your city, or even make some roads run underneath each other.
Natural Resources and Transportation
Depending on the type of city you want to build, consider adding in some interesting features that many towns don't have, such as a mine, fishing dock or port where LEGO ships can dock to load and unload cargo. Using cave formation LEGO bricks, you can easily add a mine, and there are a variety of gold, diamond or ruby pieces that you can place inside the cave, depending on what type of mine you want. Build a fishing dock by placing brown bricks across blue ones, and adding fish to the blue areas. Make a port for cargo vessels the same way, but you might use gray bricks instead of brown ones, since cargo docks are built from metal, not wood.