With young kids you gotta go to LEGO Land!!

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Harry: "I expected the Rocky Mountains to be a little rockier than this."
Loyd: "I was thinking the same thing. That John Denver's full of shit, man."

It's certainly not a four-star resort, but the excellent suggestion of Legoland made me think of the Sheraton Carlsbad. Definitely upscale for a Sheraton, and has direct access to Legoland. Not walking distance for families, but not too far from the beach. Other attractions include San Diego Zoo and/or Wild Animal Park, USS Midway, the Aquarium, Coronado Island, downtown, Padres, etc.

I'm not really sure how "upscale" any of the hotels along Mission Bay are, but if you will be there in the summer, direct access to calm beaches in Mission Bay could be really nice. Plus, endless bike path for the kids.

Balboa park has multiple museums, some of which are free. My boys loved the railroad museum. There are also plenty of gardens to walk through.

Was not impressed by the zoo. Found it to be old and dirty.

The USS Midway is a self guided tour that is a must see. Stop and talk to the docents. My kids were entranced by some of their stories.

La Jolla cove for seal watching.

The Catamaran in P.B. You're centrally located, and directly across the street from the beach.

We stayed at the Loews Coronado Bay resort. Worked well. Close to all there is to do, can walk across to the beach, has a good pool and we also took a small sailboat out in the bay. Also has tennis and basketball for the kids. You need to rent a car.

We rented an awesome VRBO condo in mission bay. The unit had a deck overlooking the bayside beach - so people could be inside or outside and still communicate as kids got tired/ hungry. The bay is so calm and fabulous for kids. It was only 3 or 4 blocks to walk to the ocean side and watch the surfers/ volleyball/ waves/ rollerbladers and some adults could rent boards and surf while others played with the kids on the beach. There were a ton of restaurants in walking distance.

We were there last March and bought a city pass which saved us a bunch of money when hitting some major attractions; we enjoyed Seaworld, the zoo, Balboa Park, USS Midway, Belmont Park, a harbour cruise, and kayaking which was all included in the city pass. The pass also included Legoland (hugely overrrated in my opinion and according to my kids too busy, long ride lines, boring rides) and Knottsberry Farm (awesome!) so we headed up towards LA and stayed a night there before beach hopping back to SD.

I will 2nd the Legoland for the youngsters, but not sure about the hotel there. They certainly charge 5* rates, hope they are actually delivering on that. We stayed at a local hotel that was 1/5 the price on a 5 day pass and had a great time. Lots of cool beaches too, some right there in Carlsbad, or south through Encinitas all the way to La Jolla. Now they have some upscale places to stay there..

Almost forgot, plan a trip to the DeSoto factory and do some shopping for the big people..