The seafood restaurant where I have always had a wonderful meal in San Diego is Eddie V's. I know, it is a TEXAS upscale chain, but I find the food, service and ambiance to be impeccable.
As a casual/laid back town, the best of San Diego is not precisely fine dining or seafood despite being a coastal city.
San Diego is known for beer. Some breweries have very decent food (not seafood though). There are breweries/beer places all over the place (check Yelp). I am not too much of a fancy person, and I enjoy places like BLAH (Blind Lady Ale House) in Normal Heights, a little bit off the touristy areas.
For a nice day out, as mentioned above, Coronado, Balboa Park are top choices, I agree. May I add LA JOLLA downtown. There is a nice park at the beach, the seals at the children s pool, a modern art museum, and numerous restaurants and shopping. The quintessential touristy upscale San Diego restaurant is there too: George's at the Coves (there is also an Eddie V's in downtown La Jolla).
But what I really miss of San Diego when I am away is its Taco Shops. I have my favorite ones, each neighborhood has their own. But not all are a good. A safe bet might be Rubio's (a chain) and its famous fish tacos.