I just took my sons to the San Diego Natural History Museum to see there exhibit, Lizards and Snakes Alive... I have to honestly say that it was definitely worth the FREE Resident admission but not worth the drive. While my 3 year old loved every minute of it... I could have just as easily took him to our local reptile store and had just as much fun. If you are planning a trip to Balboa Park make sure you hit up the other museums while you are there.
Rueben H. Fleet's Kid City was a great time and they even have an area that my little 13 month old could safely crawl around. We had tons of fun and will definitely be heading back.