My then-2 year old loved it, and I'm sure he will love it when we go again!
Looking at the dolphins in the tank where they can swim right by the "underground" window, then walk up a bit and can put hands into water.
He loved loved LOVED the Petz Rule! show. That is a DO NOT MISS show, I'm serious. My childfree brother and SIL became kids again watching that show, and they joined FOR it. They live in Chula Vista and will spend 2 hours at SeaWorld, just to see the Pets show...it's a great little show, and we all enjoyed it more than the dolphins or Shamu shows!
There's a great play area for kids, and DS loved the musical instruments like triangles...spend something like an hour there. Loved looking at the can't-recall-their-names dolphins at the Atlantis ride hanging out with his uncle, while his mama went and did the ride.
Loved seeing the Budweiser Clydesdales (and one miniature donkey).
Loved the Polar Expedition thing, though we didn't do the "experience" part of it, just walked through the line to not do the "ride". Got to see walruses and beluga whales, and polar bears...all of which are at our local zoo and aquarium, but he loves them all the same! Got to touch the ice wall in the polar area...
Saw penguins, saw manatees...
There's just SO MUCH there for a kid. Go go go! And see "Petz Rule!"
sigh...I am now rethinking the "don't go to San Diego" part of our upcoming trip....augh!