San Diego Zoo is awesome. Your plans sound great as is--zoo, Balboa Park. I would skip La Jolla (it's a bit up the coast), but that's just me. There is SO much to do in Balboa Park (zoo is there too). You easily can fill 2 days there.
Is SeaWorld on an additional day? When we do SW, we do a whole day there. If it's one of your 2 days, you're overbooked already. (I've never been to Aquatica, and I'm not sure how far away it is from the other attractions.)
I agree with PP to skip Legoland.
A couple of laid-back options: Seaport Village (to see boats and nautical shops) and Belmont Park in Mission Bay (has a roller coaster and a few other "Boardwalk" rides). Maybe Old Town too.
DS '04 "Boogaboo"
DD '08 "Lilybear"