We were just at LegoLand 2 weeks ago. It was our 3rd trip there.
Here's a coupon: http://www.sandiego.org/coupon/UK/73
And you might want to find a Costco out here, if you have a membership, as they always have deals for LegoLand and sometimes for the zoo.
We stayed in Del Mar (about 5 minutes away on the freeway) at the Hilton Garden Inn. Very nice place....not the Rtiz, but super clean and comfy. We paid $100/night there.
http://hiltongardeninn3.hilton.com/en/hotels/california/h...
Start Legoland the second it opens, since they are slow on getting people on rides and it's not open long hours like Disneyland.
SD Zoo is amazing. We had an annual pass 2 years ago. You CAN get through it in one day if you keep moving, but you are going to need every minute. There is also a double decker bus that you can get on and off all day, so it takes you to whatever you want to see. Worth the extra money if you have little ones. Parts are VERY hilly.
http://www.visitcalifornia.com/Fun-Spots/ go to SD Zoo for a coupon.
Things not to miss at the zoo are:
*Feeding the giraffes - once in a lifetime experience and bring your video camera
*Riding the skyway
*Orangutan enclosure is my favorite.
*Pandas are cool, but I believe they have specific times for viewing.
Once you get there, figure out your route and see the stuff you really want to see and then do those things first.
If you have time, go to SeaPort Village and take the SEAL tour. It's very fun and educational. In 90 minutes, you'll get a lot of the history of San Diego AND a great bay view of military training of dolphins and seals. We went on a Friday, when they were working with the dolphins, etc.
http://www.sealtours.com/index.asp