Recos for San Diego

We went to a place called Paradise Point (we got a really good deal through Expedia). 
It's a huge complex, but I liked that it had a big big room, almost cabana-style, beaches and numerous pools. 
They had several restaurants on-site, but it only took us a few mins to get to downtown and hte Gaslamp. 
All rooms had a fridge (no microwave, though).
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you should visit the "Wild Animal Park" and Marine World. My kids
enjoyed the trip and we stayed at the Marriott in La Jolla.

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if you don't mind the cost, the Four Seasons in Carlsbad (Aviara) is
great.  Nice kids area too.  You should also do Sea World - prob more
fun for him than the Zoo (which is HUGE).

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We just went to San Diego 3 weeks ago, and we visited the Sea World,
that was the highlight for both parent and kid. We stayed in Radisson
hotel ( 3 or 4 stars), which is very nice and only costs $99 a night,
it's in Lo Jolla, right next to UC San Diego, check out thislink for details.

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I just got back yesterday from a week in San Diego with my 1 yr old and
3 yr old.  Because my kids are so young we decided to devote only 2 days
to theme parks so we did 1 day at the zoo and 1 day at Legoland. 
Although we didn't get to see everything, I think it was the perfect
amount for this age but if you have older kids you could definitely do 2
days at Legoland and maybe 2 at the zoo but I would be more inclined to
do 1 day zoo and 1 day Wild Animal park which I hear is great.  Seaworld
is also worth a visit but we missed it this trip.
As for  accomodations, we rented a  3 bedroom house  in La Jolla Shores
1 block from the beach.  It was $1500 for the week and worth every
penny.  If you want info on the rental, I'd be happy to pass along the
contact info.  The guy we rented from has a few different places to
choose from.  I found his listing on http://vrbo.com.  We had beautiful
weather last week so we really enjoyed our beach time.  The kids had a
blast playing in the sand and there was a park adjacent to the beach
with a big play structure and swings.   We could also walk from the
house to a few restaurants which was nice.  Overall a great family area
and centrally located to the theme parks.