Caroline's at Scripps Institute of Oceanography - what a VIEW!
Happened to be walking around La Jolla Shores a week ago and noticed this restaurant at the south end of SIO. This place has the most spectacular view in all San Diego! And the food is not bad (brunch and lunch) and it's relatively inexpensive (about $10 for brunch items, burgers, sandwiches, salads). It's order at the counter and then delivered to your table, so service is minimal (and to get coffee refills you have to go back to the counter, which is bizarre...).
I had the braised shortrib hash and eggs ($10.50), my wife had the Mediterranean scramble ($9.50), both were very good. Very acceptable coffee. Brunch at Barbarella is probably a bit better for about the same price, but the view makes up for it.