I know the desert mountains are cool and beautiful, and not to be overlooked, but, don't think you should overlook the beach, either, which it seems, no one's really mentioned, except in passing. Yeah, if the weather is no good, certainly head into the desert. But, if it's one of those sparkling San Diego days, you should definitely take a look at a beach.
Torrey Pines is one such magical place.

http://www.torreypine.org/

Been in San Diego over 23 years (rode my bike all over this beautiful county for several years), and of all the places I have been, the East County is the most unique. The coast is where most gravitate, but if you want to see what makes my day, check out Kitchen Creek. It is beyond Pine Valley a few miles (going 40-plus miles east of San Diego on the I-8, you will see the exit most others ignore, as it goes "nowhere"). Generally closed to through traffic most of the year, unless you are hiking or riding a bike, Kitchen Creek represents what is unique to San Diego, a S. Mediterranean climate with the greatest biodiversity anywhere in the world (documented by Natures' Conservancy). Something like a 12 or 13 mile climb ends at Sunrise Highway. Check it out. You won't be disappointed.