Here's my 2 cents-

Some of the best beaches in San Diego are in North County (especially with kids) and South Carlsbad State Beach is one of our favorites. I would not base myself at a downtown hotel for beach activites unless Coronado is on your list (the beach at the Hotel Del Coronado is one of the best beaches in San Diego).

When Downtown, especially with kids, you will really miss a great opportunity if you overlook the Maritime Museum (and pay the extra $3 per person for the harbor cruise on an old Pilot Boat). It is a great value (lots of old ships and two submarines to explore) and not very expensive.

You keep referring to "the park" - do you mean Balboa Park? Not sure what the attraction there would be for younger kids, unless you want to go to the museums (Air and Space and Science Center, maybe Natural History). San Diego has a lot to offer other than commercial pay-admission venues.

Please look into the Cabrillo Monument. $5 per carload for admission, the lighthouse is worth seeing and the tide pools at low tide are the best in the city. If you time it right, you can have a family meal at the Corvette Diner at Liberty Station on the way to/from the Monument.

The glider port at Torrey Pines is free and it is exciting to watch the Parasailers jump off the cliff. You could stop there on your way South. The town (village) of La Jolla does not have much to offer kids other than seeing the sea lions that have occupied the Children's Pool, though the beach at La Jolla Shores is family friendly (it is north of La Jolla proper). The Birch Aquarium is also well done and is right near the glider port.

I wouldn't go to the Wild Animal Safari in August, even if you get there when they open (and I prefer that Park to the Zoo) - plus you have to pay for parking there so if you only go for a half day it all adds up.

You have not mentioned Sea World, which although it is more commercial now, still has great educational as well as fun opportunities and it is a well run and beautiful park. Bring a change of clothes for your kids and let them get wet!

As mentioned, you can get great deals on Zoo, Legoland, and Sea World tickets though Costco. There is a Costco adjacent to Legoland (and they also have beach chairs and umbrellas). An inexpensive family meal is to do take out Pizza and salads from the Costco food court and bring it back to your hotel.

There are lots of fun restaurants in the Carlsbad area. I would not be inhibited by the traffic from Carlsbad going south. I live in Leucadia and it is not bad after 9 AM. You will have the use of the carpool lanes coming home and it makes a big difference (and your kids will probably be asleep from all the activities!)

Other things to consider in North County are the Ocenside Pier and harbor & the Museum of Making Music (put that in for info purposes for others who may be reading this with older kids too), (I second the Mission at San Juan Capistrano - very worth seeing).