I recently made a visit to the zoo after probably ...

I recently made a visit to the zoo after probably a ten year absence. However, in that time, I've visited the Safari Park a couple of times. After this most recent visit, my opinion remains the same - the Safari Park is the better experience.
If you have the time to do both on a San Diego visit, certainly do so. But, if you have to pick one, spend the time to head out to the Safari Park. While the zoo is large, it's not so different in layout from other zoos that I've visited.

One thing we ran into a lot of - no animals in sight! Most of them were hiding away in shaded areas where they were not visible. Several sections could really stand a redesign so that, even when the animals are in the shade (and they were the smart ones, it was hot!) they can still be observed. The visit was mostly a disappointing walk from one enclosure to another with few signs of animals. The Safari Park does a much better job of allowing you to actually see the animals.

One of the big features of the park is no longer in play - the Chinese Pandas have been returned to China. The party that I went with was particularly interested in seeing these and the decorating around the area is still adorned with them - but they're gone.