Will be a great trip! I live in SoCal, grew up in NorCal, and have a 5yo and 3yo... so I think I can relate.

In the broadest terms...

The LA->SD trip offers you a lot of kid-oriented stuff from Disney to LegoLand to SD zoo to beaches, etc., and with less driving. (Anaheim->SD = 80mins.) SoCal has it's own beach-oriented beauty, but is definitely different from Central and Nor Coasts: more people, more development.

The SF/LA trip still offers some of the same kid stuff, but you're smart to plan for at least 2 days to make the drive comfortably with the little ones. Total drive time, with zero traffic, you can do it in 5 hours on Interstate 5 (but it's not scenic). US 101 and US 1 are much more scenic, but are less direct and fast, esp. US 1. Central Cal is more rural and quieter than LA/SD areas.

Nevertheless, a beautiful trip could be comfortably done with stops/stayovers in any number of towns including Ventura, Santa Barbara, San Luis Obispo, Paso Robles, Cambria, Carmel, Monterey, Santa Cruz. And, I'm sure you'll agree, you don't need a Disney experience in each of these places for the young kids to have fun... nice local playgrounds and beaches are about all they need at this age!

In any case, please share more specifics about things you'd like to see and do... or at least the types of things (e.g., amusement parks, beaches, hiking, etc.).