I see that this thread has gone a bit off the rails, but I'll try to answer the question posed in the original post. I've played Torrey South at least 100 times, mostly between 2001 and 2005 (it was $10.50/month for junior golfers in San Diego). Needless to say, I've thought a lot about the course, what I liked, and what could be better.
The setting is beautiful, and at a macro level (i.e., if you zoom out and just think about the general hole corridors), the routing is really good, making good use of the cliffs and canyons. As others have noted, a lot of the holes and greens don't get as close to the cliff and canyon edges as you might like, and some of this is surely attributable to environmental regulations. It would be great if they could push the greens and fairways a little closer to those edges so that the natural setting is a bigger part of the strategy and the golfing experience.
The greens, bunkering, shaping, etc. are very unnatural. The course could be a lot better with more natural/minimalist greens and green surroundings.
The course doesn't have enough subtlety or charm. For example, in contrast with other U.S. Open venues, there are no exciting, interesting short par 4s. The 2nd hole could be a good candidate for this if it were a little shorter and had some more interesting features (perhaps with a smaller, more exciting green). 10 is a pretty uninteresting hole where you have to backtrack a ways to get to the back tee, so that would be another good opportunity to try to build a more interesting, shorter par 4.
As far as individual holes go, I think 3, 4, 7, 13, 14, 16, and 17 are very good and could be even better with some tweaking along the lines mentioned above. Other holes are either forgettable (1, 5, and 10) or downright bad (18). The artificial pond and the artificial green on 18 are a terrible way to end the day on a seaside golf course.
Despite my sentimental attachment to the place, I suspect you'd have to go back pretty far in time to find a U.S. Open being played on a worse golf course. The sad part is that it could be great, and you wouldn't have to meaningfully change the routing. You'd just have to build some interesting greens and bunkers that fit the terrain, and you'd have to be willing to use the edges of the cliffs and the canyons a little bit more.