On the way from Phoenix to San Diego, you might want to check out:
Yuma Territorial Prison State Historic Park
Imperial Sand Dunes
The Salton Sea
Anza-Borrego Desert State Park

Once in San Diego, make sure that one of your first stops is at Balboa Park. Not only is this the site of many of the best attractions in San Diego, but it has a very helpful and friendly staff at its Visitor's Center. Then there are the town's major attractions:
San Diego Zoo and Wild Animal Park
SeaWorld
The Padres

In any event, this should be a good trip - Enjoy!

AZBuck