I agree that SD golf is not what it could be given the land, weather, and number of golfers. However, I think SD courses do not get their due credit.
My top 4 in the metro area are Torrey South, San Diego CC, Rancho Santa Fe GC, and Pauma Valley CC. SDCC has some of the best greens in the world with incredible natural undulation and impeccable conditioning. Rancho and Pauma are also good classic designs with good greens.
La Jolla is fun and scenic but not as good as my top 4. Some of the modern private clubs like The Crosby, The Bridges, The Farms, Santa Luz, Fairbanks, Del Mar CC, Morgan Run, Del Mar Meadows (new name now but I can't remember it) are very fancy in terms of conditioning and amenities but very weak architecturally. Additionally, most of these courses are unwalkable.
SD is also pretty weak on the public front. There are very few good public options and pretty steep greens fees. I think Torrey, Barona, Carlton Oaks, and Cross Creek are probably the best of the bunch (factoring in price).
I agree with the overall sentiment of the thread, but I hold that SD does have 4 very good golf courses, and there are only a handful of cities that can say the same