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It's not convenient to anywhere in SD expect Shelter Island. If you're planning to go somewhere in SD every day and/or like to go back to the hotel for midday breaks, it's not a good location.
Convenient to what locations? Its near the airport, so if you have a rental car it is convenient to get back to the rental car location and airport. Its also convenient by car to anything around the airport, but not convenient to say The Safari Park. "Convenient" is kind of relative to what you are doing.
I haven't stayed there, but Shelter Island is beautiful on a sunny day. How close it is to things depends on what you plan on doing. It's a short drive to downtown/Coronado/the airport. The Zoo really isn't too far, but you have to expect to drive to everything. That can be said about anywhere you stay in San Diego pretty much.
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