Maybe it's just me, but I would skip the zoo in favor of Wild Animal Park and/or Sea World. To me, the zoo is just okay. We had SD Zoo membership for a few years and it didn't cost extra to go but we would usually go to WAP instead. I just like it more. The zoo can get very crowded during high season. And hot-don't be fooled by the weather in SD. They take the temp at the airport which is on the ocean. The zoo is always hotter in the summer than the weather forecast. Of course, so is WAP but at least you know it'll be hot.
If you do the zoo, definitely ride the bus. We like the one you can jump one and off of. Cuts down on walking all those hills.
Have fun whichever you choose.
By the way, if you are thinking of doing both the zoo and WAP then you might want to check out becoming a member of the Zoo. It's pretty reasonable, for example, $89 for dual adult membership, or $109 for out of area. Kids are $24 or $28, depending on age. The membership inc. free parking, free rides on the skyway at the zoo. Discount on the bus tour. Also includes free guest passes as well (adult membership only). Also, membership is 100% tax deductible.
I just checked WAP website and a 2 park adult tix is $60. So if you have 2 adults it would cost $120 for both. Plus parking at WAP (inc. with membership). Membership would only cost $109 and inc. free parking and free skyrides (reg. $4). The kid's memberships are also a great deal.