Beware!!!
When you "hug" the Coronado side of the bay in the area of Shelter Island there are some hazards we need to watch for. Examine the charts carefully. Most the shoal areas are plainly marked, but there is a submerged dock toward the south end of Coronado as you head into open water, before the submerged rock jetty that runs out past the point on the Coronado side. I know a couple of people who have run aground on it when the tides were just right.
Also with hightened security around the naval base and aircraft carriers there will be added patrol boats to keep you away. Then there is the problem of the kelp bed. If you stay to the east side of the bay opening you won't have any problems with kelp in your keel or rudder, but if you decide to turn north toward Mission Bay, La Jolla Cove, Scripps areas, and the rest of the California coast, you will need to get out past the San Diego Bouy #1 before turning, elsewise you will find that you may be traveling through heavy areas of bull kelp. There is a kelp harvesting company that operates out of the bay and is located very close to the Coronado bridge on the San Diego side of the bay and many times the kelp is cut down, but I don't like to take to many chances in that area because of the heavy traffic going in and out of the bay.
Then there is the Mexican border. Many people don't realize it, but if you sail out of the bay toward the Coronado Islands that you can see on a clear day you are actually heading due south. If you keep sailing toward the islands, which are only 15 miles out, at some point you will be in Mexico and subject to their laws and regs. If you have anything on board that even resembles fishing equipment you will need Mexican fishing liscenses for the boat and everyone on the boat. If you are carrying a large party of guests that could become expensive.