Do you want to spend the day running from show to show, or just walking around and exploring? At Sea World it seems like the show schedule really dictates your day, while the zoo is much more kick-back.
I enjoy both parks, but it really comes down to what your preference is. Some people like the marine animals more, and for those, I would heartily recommend Sea World. For those who prefer land mammals, go with the zoo. They're both so much fun, and both are worth the cost of admission. Go with what you like!
I don't know about the zoo, but I know at Sea World - you can go on tours (they'll cost ya!)
I've been on 3:
Penguin Encounter: It was tons of fun, you get to learn about the penguins, pet one, and then go behind the glass where they live. I think it's around 20 something dollars per person and I believe it's a seasonal thing so check first.
Dolphin Interaction Program: This program is pricey but really fun. SeaWorld provides you with wetsuits, shower area, soap, ect. It last about 60 minutes and you MUST bright your swimsuit as well, you can't have any jewelry on. You get to jump in the water with the dolphins, they take a picture that you can buy, ect. This will cost $170 per person.
Wild Artic Interact Program: I LOVE this and would recommend for anyone who is able to participate to do so. Details: You need to sign a reliability release, you should be comfortable in chest deep water, program last 70 - 90 minutes, you are required to wear a SeaWorld issued wet suit with booties (you'll be glad...), you must bring a swim suit, and remove all jewelry. This is the site's description: "Immerse yourself in a whole new world where you’ll make new friends with barking seals, massive walruses and huge polar bears. You won’t believe the overwhelming power and majestic grace of the beluga whales as you slip into your wet suit and become one with these awesome animals in the Wild Arctic Interaction Program. If you’re planning a visit to San Diego you won’t want to miss this once-in-a-lifetime encounter with animals from the Wild Arctic." This will also cost you $170 - but in my opinion, it's totally worth it.
Oh, and if you don't know what a beluga whale is...it's this cutie:
And they are tiny compared to the killer whale...
Beluga Whales are on average 32 feet.
On average they weight 7 tons.
On average they live 75 - 100 years.
Oh, and they are carnivores - but rarely attack humans.