I have to disagree, but that is of course just my personal opinion. The gorilla enclosure has been criticized here before. I remember it so full of electric wire, that gorillas had problems to move without getting zapped every few steps. It was extremely expensive, in large part due to this stupid waterfall. Many other enclosures at other zoos are way better. The bear grottoes really are bad - no substrates, very small and so on. Yes, giant pandas and koalas are very high profile, but they are also among the most boring species possible and at least the way the koalas are presented is pretty dull as well.
Question is, do you have to have the biggest collection to be the best (top) zoo ? Even for the price of some very rare species in some pretty bad cages? The Berlin zoo and Tierpark are examples of zoos with similar problems. Others are not as big but overall way better. Personally, I would rank Woodland Park or Bronx higher than San Diego and I have not even been to Miami or Audubon which have a pretty good reputation as well.