The car museum is excellent! But you need to go to Symbolic motors in La Jolla. And the fun part, they are all for sale! Drop off your wife to go shopping in La Jolla, and then drive to Symbolic.
Kemosabe's (
http://www.cohnrestaurants.com/restaurants/kemosabe/) in Hillcrest has good food, good wine, and will be casual enough for the kids. If you like hot spicy food, get "Skirts on fire". And the Winelover next door used to be the best wine bar in San Diego.
A few other things to do: The Hotel del Coronado. "Some like it hot" was filmed there. Good cheap fun, go to the end of Point Loma during low tide and look at the tide pools for organic sea life.
Remember, the water on the west coast is cold. Even in the height of summer, it is cold. If you are at the Mission bay Holiday Inn, you might want to hang out on Mission Bay, where the water is warmer.
And everynight, Sea World has fireworks, all summer long. I would avoid "Old Town", since it is more of a tourist trap without much.
IF you can ditch the kids for a night out for Adults, go to the downtown area, "The Gas Lamp District". Take a cab and then walk around. My favorite bar was "The Bitter End". There are lots of places for dinner, and music, and the rest.
Do not even THINK about going to Tijuana. It just isn't safe these days.