The San Diego Zoo is good. I have also been told the San Diego Zoo Safari Park is good. We did the Zoo last year and I think we may do the Safari this year. As an FYI the Safari is not located near the Zoo, it's about 30 miles away.
The Midway is fantastic! You won’t go wrong there. The Maritime Museum is right up the street from the Midway. The Safari Park is great, but it’s east of Escondido. If you do happen to go, the San Pasqual Battlefield is on the way but only open on weekends. The kids would probably hate it, but a great piece of history. The San Diego Zoo is an amazing zoo. You can also do the Skyfari at the zoo, like an old school trip on the Disneyland Skyway! The Aerospace Museum at Balboa Park is one of my favorites and close to the zoo entrance. The Hotel Del Coronado is a gem and Coronado is a great place to visit. Finally, Cabrillo National Monument will give you great views of downtown San Diego and Coronado.
The Midway is great! If you want to make a day of it you can walk from the Midway along the harbor to Seaport Village and then to the Embarcadero and Gaslamp Quarter. There are all kinds of great restaurants, from touristy (like Kansas City BBQ, the bar from Top Gun) to fine dining. The Zoo and Balboa Park (gardens and museums) or the Safari Park (up in Escondido so allow for an hour travel time) are also great options.
We just got back from our CA trip and spent 5 days with our cousins in San Diego. We loved going to Point Loma and seeing the Cabrillo National Monument, the lighthouse and tide pools. My 14 year old twins thought the tide pools were the best part of our trip. We also enjoyed going to Old Town and having lunch at Cafe Coyote.
My DS12 loves snorkeling at laJolla cove. The parking is horrible and the smell even worse but where else can you get so close to Sea lions?? We have been to SD twice to visit my DD. The zoo is fabulous too, best one I have ever been to. I second Seaport Village if you go to USS midway.
We love heading to Coronado Island. seeing the Hotel Del Coronado, an old beautiful hotel that the Grand Floridian was modeled after (I’m pretty certain). There is a nice beach right at the hotel too, and is located amongst some darling cottages, and palatial beach homes. There are restaurants and shopping, on-site, and nearby.