I know this is an old thread, but as a member of the SD Zoo, I felt like chiming in. I see both points of view, although I think the negative group is way too caught up in little details.
The best attribute of the zoo is probably the sheer amount of species, but most of its exhibits are somewhere between good and great.
I would break their exhibits down this way:
Positives:
Gorilla Tropics(tremendous imo)
Monkey Trails(very good assortment of animals and viewing, isn't as good as it could have been though)
Absolutely Apes(I can agree that there could be more options for the apes as far as climbing/swinging/being in the canopy is concerned, but it's still a great exhibit.)
Ituri Forest(I guess I just don't care about the fence much, also not nearly as bothered by the otter/buffalo exhibit as most.)
Tiger River(very good exhibit, saw the cubs up close on my recent visit)
Pandas(very good, but I like DC's better because you don't have to wait in a line.)
Polar Bears(Great imo, btw, no red pandas in that area anymore.)
Sun Bear Forest(also very good, just put a couple youngsters on exhibit)
Reptile Mesa(tons of animals, the tortoises and Indian Gharials are highlights)
Hoofstock(Obviously beat most zoo's in quantity, most exhibits are spacious enough as well, will be interested in what they do with the space that the elephants are currently in(hopefully rhino's or giraffes, then combine the two exhibits those two use for the other species.
Koalas(Has a bunch of them, successful breeding, good viewing)
Aviary's: A couple good one's, although I'm not that into birds)
Raptors(good, spacious enclosures for various eagles and condors.)
Plus some random other exhibits like the Giant Anteater, meerkats, tree kangaroo's, and birds of paradise. And again, the sheer number of animals is a plus, even if some of the animals aren't in good exhibits.
Elephant Odyssey to come, looking forward to seeing this one, will surely be a positive for the elephants, and almost as importantly, the lions and jaguars, which brings me to the negatives.
Negatives:
Big cat exhibits other than Tigers(They do have the space to upgrade the exhibits right where they are, especially with the jags moving, hopefully that's next)
Bear canyon(Not horrible, but would love to see new exhibits)
Rhinos(addressed this above in the Elephant Odyssey part, would like more space for them, there is good viewing however)
Various smaller animals(many are still in old school cages with little space)
Overall an excellent zoo. I certainly get the frustration, some zoo's, mostly the newer one's don't have the issues the SD zoo does. However, most also can't compete with the amount of species, including rare and exciting one's, and also can't compete, or at least beat the best the SD zoo has to offer in terms of exhibits.