LaJolla Marriott is more business oriented with lots of office parks nearby. There is a shopping mall across the street and you can walk around a bit if socal suburbia is of interest to you. This may be an option if you plan to drive around (sea world, legoland, la jolla/del mar etc) and not focus on SD itself.
Downtown location is better if SD itself is your focus and you can usually find cheap garage parking nearby if you hotel is not reasonable in that regard.