I got back last month after our first trip to SD. Don't know if you drink but I'll add some of those as well.
Keep in mind that we had a rental car for 2 days and did Uber the rest of the time.
Since I was forcing my wife to go to so many craft beer places I thought we'd start with something she liked. Drove up to Temecula and visited a few winery's. Had an excellent lunch at a place called The Goat & Vine.
Didn't eat anywhere fancy the whole time we were there.
Breakfast
Kono's Cafe-Excellent. Right on the water. Huge portions.
The Mission(J street)-Food was good but my god they have a homeless problem in this area.
Snooze-Excellent
Lunch or Dinner
The Taco Stand-Lajolla-Be prepared to wait in line but very good
Oscars Mexican Seafood-Fish Taco's. The best I've ever had.
Pizza Port OB-Good pizza/Great beer-Very casual
Things to do
Really enjoyed going on a 3 hour sailboat (Sail San Diego)
Zoo
Midway
La Jolla Cove
Bars/Breweries
4 star-Toronado Bar, Modern Times,Stone
3 star-Belching Beaver, Rip Current,Societe,BottleCraft
Things to skip
I wouldn't go back to Coronado
If you go to the zoo it includes a bus ride around the park. DO THIS!!!! We didn't and ended up walking about 20 miles.