We did a 3.5 week trip a few years ago with similar aged children, flying in and out of San Diego. Lots of driving but we wanted to show the kids as much as we could in the time.
SD - get over jet lag, the zoo and Balboa Park, La Jolla.
LA - Venice Beach, Muscle Beach / Golds Gym (for eldest DS), Santa Monica pier, Griffiths Obs, Walk of Fame, Universal Studios.
Big Sur, Hearst Castle, San Simeon elephant seals, Morro Bay, Carmel, Monterey, Santa Cruz for the boardwalk.
SF - Fisherman’s Wharf for sea lions, Alcatraz (book well in advance), general walking around, Golden Gate Bridge.
Lassen Volcanic NP (my favourite) and then down to Reno (over the top casino stay).
Yosemite - Bodie ghost town, drive through the park, a couple of short but spectacular hikes. Kings Canyon - like a mini Yosemite but much quieter. Sequoia NP.
LV - Death Valley, Vegas, flight over the Grand Canyon, Hoover Dam, Lake Mead.
Palm Springs - Joshua Tree, San Andreas fault and a water park.
Back to SD to fly home.