If you are visiting San Diego, then you will need to consider what kind of ground transportation is available to you. How will you will get around town once you've arrived?
If you want to "see everything" and can drive, then I highly recommend you rent a car. The entire city of San Diego is built on a series of interconnecting highways so renting a car will give you much flexibility and allow you to come and go as you please.
If you want to tour San Diego at a relaxed pace or cannot drive, then I recommend a taxi along with a bus tour. Taxi drivers in San Diego are honest and will deliver you to your destination with minimal hassle. Tours are worth their price: they show you the highlights and provide information that you would otherwise have to search for by yourself. Read about: