An old friend asked me for some recommendations, I thought I'd share what I sent them here. They have a car and don't mind driving. Budget not an issue. "Real" food that locals eat is the theme they like.
San Diego has an odd blandness in terms of cuisine. There is plenty of good food here, but no cultural food identity like you have in places like NYC, San Fransisco, New Orleans, Boston, Chicago, Seatle, etc. In general, folks in San Diego eat just to fill their tummy, even when they go out. So don't expect something wild.
Having said that, here are some things locals eat which are absolutely worth trying.
The fish taco is our unofficial city dish. It's nothing fancy, and if I want a really good one I make it myself. But these are good -
Rubio's - It's a huge chain, but they make a tasty fish taco. Other things there are average at best.
Mariscos El Prieto - My personal favorite. Worth the drive, try the marlin tacos too.
The other thing we do well is craft brewing. There are tons of breweries here, and competition breeds quality. Be sure to grab some local craft brews if you see them on tap.
Brew pubs - Be sure to ask for local beer recommendations. All of these have good food and beer.
Blind Lady Ale House
Tacos El Paisa - Great place to have some street tacos and beer. I love the al pastor here.
Rudy's Taco Shop - Get the mini-street tacos, especially the carne asada.
Mariscos (Mexican seafood) - I prefer the trucks, but you'll eat standing in a parking lot. Which is fine.
Mariscos German Beyer - Don't let the neighborhood frighten you. Damn good tacos.
Mariscos Isaac - Everything is good here. Nice tacos and ceviche. Try a seafood cocktail.
Banh Mi - Great Vietnamese "to-go" sandwiches. Just get the BBQ pork.
Bale French Bakery
Fishery - Upscale.
Blue Water Seafood Market & Grill - There will be a line.
New American -
Urban Solace - Interesting take on classics, quality food.
Cucina Urbana - Suggest reservations.
Food trucks - Best to find a multi-truck event. Check this site for events and locations - http://sdfoodtrucks.com/
My favorites - Super Q Food Truck, Devilicious, New York on Rye.
Cafe Chloe - Bistro style
Cowboy Star - Upscale steaks.
Linkery - Farm to table.
Blue Ribbon Artisan Pizzeria - Upscale craft beer and pizza.