Another opinion on Soak City-
Palm Springs-never going there again. The theming is basically how much concrete can we use? And don't even get me started on the food! Expensive, gross, takes for every to get. Also Knott's doesn't allow any outside food in. Too bad.
Buena Park-better than PS but still not that great. The lazy river is pretty much a joke. Have to be in a tube and when it's busy, or the employees show up late to work, they make you want, in groups, to enter. Add you had to be in a tube, no swimming allowed. Only reason we went was we had a Knott's AP and I added the SC option. I won't make that mistake again.
San Diego-haven't been, don't plan on ever going after doing 2 of them.
Tubes at SC will cost you extra. They have some for free but if the park is busy you'll have to pay for them.
Biggest problem with SC is it is not a Disney waterpark. We love BB and TL at WDW! The best! The theming, the rides, the food, all of it.
There is one other waterpark in O.C. Wild Rivers in Irvine. DD's Girl Scout troop went in late May last year and the girls loved it. It still wasn't as nice as Disney, but much better than Soak City. Their lazy river was much better than SC. And so much closer than San Diego. Actuall SC San Diego is located in Chula Vista, almost to the Cal/Mexico border. 110 miles from DLR.
I would take the bus to the Zoo (or how about Wild Animal Park-which we love) but I wouldn't take the bus another day to go to SC. That's alot of time on a bus. If you are going to take the bus to SD twice, have you considered getting a rental car for 2 days. It may be cheaper than the bus.
Instead of SC how about Knott's Berry Farm? It's actually a pretty nice park, contrary to many opinions here on the board. No, it's not Disney, but it's good for what it is--America's 1st theme park. And the fried chicken is really good!
If you are set on going to a Soak City, go to the one in Buena Park. You'll save about 3 hours travel time and you could still have Knott's fried chicken!
Have fun no matter what you do.
Oh, weekends at the zoo will be more crowded than weekdays. I would go on a weekday. Don't know about SC but I would think the same.
On more thing, based on your ticker it looks like you are going in early June. Be prepared that the weather may not participate in your plans. They don't call it June Gloom for nothing!

While today is will be in the 90's, early June may be cold and gloomy. The day we went to Wild Rivers it was pretty much cold all day. Spent a lot of time in the "warming pools"