OK, that helps!
I also have two girls, though mine are a bit younger, now 6 and 4. We have been to the SD Zoo twice and Sea World 5 or 6 times. Both of my girls really are big animal fanatics, but really we get way more out of Sea World each trip than the Zoo. But your family may be a bit different so here goes:
Zoo: really great, up close animal viewing of a large variety of animals. Nice children's area with a petting zoo (goats and sheep mainly). If you catch feeding time at a few of the exhibits you get to see a lot of animal activity and my girls could sit and watch for a while...but it can be really crowded so even though little ones can usually get up to the glass, you can get pressed against/moved along etc. The big con is that there is a LOT of walking between exhibits, and a lot of it is up and down steep hills. The polar bears, which were a huge draw and must see for us...huge loooonnnngggg hill...so steep it took two of us to push the double stroller up and so steep down that I had to keep it tilted way back with the front wheels way off the ground so the girls wouldn't fall out, even strapped in. NOT fun either way. Pandas....looonnnnggg line and you have to be really quiet in there. It ended up being way too much downtime between animals for my very active 4-5 year old each time we went and we never made it more than about 2-3 hours before a major had-to-leave meltdown happened. So not worth it for us, and we have skipped it the last few trips.
SW: the shows are great and just the right length...my kids have sat spell bound since the youngest was 18 months. The Pets Rule show is a huge favorite, as is the daytime Shamu show (the night time one was tooo loud!). We love Breakfast with Shamu--great close up whale interaction, and the food is good too. The Arctic Exhibit is wonderful and we could spend hours in there and it is set up so nicely so you can go at your own pace and there is always a new animal just around the corner. The starfish and manta rays exhibit is fun and hands on, the manatees are our FAVORITE and there are a few rides to keep it fun too. Sea World is just our perfect day...shows and hands on stuff plus rides...we could spend days there. Oh and the Clydesdales if they are still there, they are a big hit too. We never seem to get it all done and could easily spend two days there.
Not sure if you thought about it, but we usually choose a day a
Legoland now over the zoo. It is just about 25-30 minutes north of Sea World in Carlsbad (where we stay) and your girls are a perfect age for it
if they like rides.
