Lucha Libre taco shop is in Mission Hills right near the airport- Go early and get the Surfin California burrito. The Hillcrest area is great for walking around, it is probably the closest thing to the Short North that they have. Chocolate has some nice bistro Italian food and there is an Ethiopian place that has a killer good and cheap lunch buffet. (Sorry, for the life of me I can't remember the name) There are also a ton of cute shops with vintage clothes, records and art.
Stay away from Whisk and Ladle or Prep Kitchen- both are super disappointing despite what the locals will tell you.
If you have access to a car and feel like taking your life in your hands, Mira Mesa is chock full of Vietnamese places- most of them good and cheap. Claremont Mesa is more or less Koreatown- if you are looking late night you can try BBQ Chicken which does Korean style fried chicken as well as other Korean favorites. Down the street there is a place called Tofu House that serves pretty much nothing but variations on soontobu- a spicy broth with super soft tofu.
Even further up the road in Encinitas is Stone Brewery and they give tours.
Again- not kidding about the life in your hands driving thing. Be ready to merge off exit ramps at 70 mph, California lane changes (not pausing when crossing 5 lanes of traffic) and more general insanity.
If you haven't done the touristy thing, take a harbor cruise around Coronado. :)