Going to San Diego at the end of April with my nine year old son and meeting up with my brother, sister in law and their two young sons (ages 2 and 4). We will have 3 full days and plan to go to the Zoo and Sea World. Since we'll have a rental car we may also spend the third day in La Jolla or one of the other coastal towns north of the city. We are staying at the Hyatt Islandia in Mission Bay, which unfortunately gets some pretty negative reviews in the Rants and Raves section of this website!! oh well.
Has anyone stayed at this hotel and LIKED it??? Any suggestions for places to go other than the ones I've mentioned?

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Although we had read many neutral reviews, we found the horel to be very good, and well worth the money we spent. The rooms were clean, we were upgraded for minimum fee with a beautiful view. The staff were very friendly and helpful. Overall, a brief, but very nice stay. Would stay there again!

Click here for more information on Hyatt Regency Islandia from TripAdvisor.

Only one review but it was positive. Sorry we have never stayed at this particular hotel ourselves.

This is the review on the local paper website. I've never stayed there but it is a good location (Sea World is just across the street) and sounds to me like it would fit your needs well. I think you can even go to Sea World in the morning, head back to the hotel for naps, then go back for nighttime Sea World without any problem (they used to have a stamp so you could return - probably still do something similar). Do you like sailing? They have their own marina. Down the road is a park the kids would like and Mission Beach (they have a carousel)

http://sandiego.citysearch.com/profile/86316

I think the kids would enjoy a boat trip - even if it is just around the harbor. There is also a tour bus/boat that we saw while we were there. It is an open air, amphibious tour bus type of thing. We saw it driving around town and sailing around in Mission Bay. It looked kind of strange, but interesting.

We spent an afternoon at Point Loma, just west of the harbor. Your kids might enjoy that. At the top of the hill there is an old lighthouse, good for a quick tour, a visitor's center, the Cabrillo Monument, and some absolutely incredible views. We watched the ships going in and out of the harbor and watched for whales from the lookout. Just down the hill on the ocean side are some great tide pools, with a couple rangers around to tell people about the wildlife.

If the kids are animal fanatics, the Wild Animal Park is fun, and a different experience than the zoo since you view the animals in a much more natural and spacious environment as you ride around in a tram. But three animal-oriented attractions in three days may be too much for you! Our kids though loved all three attractions and I'm glad we did them all. Sea World was our favorite and was just plain fun for the whole family. The zoo was so crowded during our visit that it was hard to enjoy many of the exhibits.

I know it's very touristy but go to Balboa Park. Loads of museums ,next to the zoo and very kid friendly. Also Old Town San Diego is neat. You could take the ferry from downtown San Diego to Coronado Island. Birch Aquarium is nice in La Jolla and see the caves at the beach there too. Also visit the city of Del Mar. My mother-in-law lives in La Jolla and we go down there once a month. Have you ever tried staying at a Holiday Inn Express? There is one in Encinitas I think and they are very clean and kid friendly.

Thanks everyone! lots of great suggestions!