You certainly make a good point, but I don't count the hotel, golf course, amusement park, and waterslide park as part of the zoo at all, though they do make for an attractive overall vacation destination!
Look at it this way: The San Diego Zoo is either the best, or among the best in almost every major category that a zoo can be rated. Very unofficially (according to our book), the SDZ is rated #1 in the USA for Birds, Reptiles, Primates, and Bears. It is #2 for Rides, and among the Top Ten for Shows, Insects, Australian Animals, Asian Animals, and Cats. No other zoo comes even close to such amazing diversity or excellence in their collection. No zoo is perfect, including this one, but it's the only zoo in America that can compete head-to-head with Sea World and Disneyland for tourist dollars, and it's very likely that it will remain this way for decades.
I seriously don't see Elephant Odyssey as a "disaster". It's a bit disappointing from the initial photographs I've seen, but having been taken through the exhibit before it opened, I think it will look fine once the dust settles and all the bugs are ironed out. I won't be shocked if, 5 years from now, we're all talking about it as one of the best and most innovative zoo exhibits in America.