As for San Diego, most of the touristy places are already mentioned, but being the most favorite city I had ever visited in the USA, I thought I throw in my 2 cents.
Sea World is a great place to visit, but when I was there myself, it took me a whole day to see everything I wanted to see.
Mission Beach is worth relaxing - it's quite near to Sea World.
Nearer Downtown, Balboa Park with its zoo, museums and the Prada will take a full day, with me it took two days to see the best of it. Then there is is Gaslamp District in the city itself.
The Trolley takes you to the Mexican border, where I spent the day at Tijuana, the Mexican frontier town.
For LA, the best place to stay, I would think is Santa Monica, on the Pacific coast. Hollywood Studios and Disneyland are nice places to visit, although they are crowded with tourists.
It is my opinion that San Diego offers much more for the size of the city compared to the size of Los Angeles.