Just got back and had an AWESOME time.
Did the Midway tour. A neat, thorough, go at your own pace "museum". Tons of aircraft if you're into that, and plenty of access to most of the ship if you want to explore. Get the headset/audio-guide (free). They did a great job of explaining what you were looking at, how it was used, etc.
Rented a convertible and drove all around. Coronado, Point Loma and the Cabrillo monument, up to La Jolla to check out the seals, sea lions, and a different coastal "look" than what SD has. That was an AWESOME idea.
The farmers market was in Little Italy on Saturday. Not sure how often they set up there but apparently it moves around to multiple spots during the week/weekend and every spot is cool and fun. We had a blast walking around it, eating street food, and getting samples from the farmers. Totally different feel and tastes than a farmers market in Texas.
Food:
Seriously, this is now one of my favorite destination food towns. Sea food, Mexican, Asian, Italian, breakfast joints, you name it. The town is awesome in the food department.
Our food highlights:
Bencotto Italian Kitchen - Little Italy
Two different locals told us this is their new favorite and it didn't dissappoint!
Cafe 222 - South area of downtown convenient to the gas lamp district and the convention center. Awesome breakfast including the famous peanut butter and banana stuffed French toast.
Richard Walkers Pancake House - Another breakfast joint in the same vicinity as Cafe 222. Insane good pancakes. The Dutch cinnamon apple pancake is ridiculous.
Top of the Market Fish Market and Restaraunt - right on the water, across the parking lot from the Midway. Excellent sea food and dessert.
Taka- sushi and other japanese cuisine in the gas lamp district. Easily (by a mile) the most fun dinner we had. He sushi was excellent! Go for dinner on the weekend, get a table on the patio and people watch. It's across the street from some happening places, the weather was awesome, the wine was great, the people were hilarious. It's at a really interesting confluence of foot traffic and there's never a dull moment (or at least there wasn't last night).