Our kids are 7, almost 6, and almost 4. We live in Southern California, so we've been to all 3 of the San Diego parks several times. We could easily spend 4-6 hours at the zoo, I HIGHLY recommend doing a kangaroo hopper bus pass - you can ride the bus all over the park and there are 8 stops that you can hop on and off as you want. The zoo is very hilly, lots of walking. Balboa Park has lots of great museums, you could do the zoo & a museum in the same day. The Space museum is a lot of fun for kids.
The Wild Animal Park is in north San Diego, and it is where we go the most since it is a closer drive for us. It's much more spread out than the zoo - lots of open space for the animals to roam. Again I'd say 4-6 hours is reasonable if you do the tram ride (the best way to see the most animals). You could spend longer there if you like to walk a lot. It is hotter up here, so depending on when you travel figure it'll be 10-20 degrees hotter than the zoo or sea world.
IMO, Sea World is a PACKED day, especially if you ride the rides AND watch shows. We could easily spend 6-10 hours there.
We haven't done Universal with kids, I'd say it would be a fairly full day. There is the City Walk mall right outside it if you want to add shopping on to your day.
For San Diego hotels, Mission Valley area is probably the most central, and there are 2 huge malls there (Fashion Valley is great). You could stay downtown, but it's a little harder to negotiate and the hotels are probably a bit more expensive.
HTH!!
Alyson