I grew up in San Diego, and I'm planning a trip back next summer. Hopefully I can help.
First, you will absolutely need a rental car. San Diego is very spread out and the public transportation is very limited. If you are only going to be doing
Disneyland/Ca. Adventure in LA, you probably wouldn't need a car up there. DL/CA are right next to each other, with tons of hotels within walking distance or that have a shuttle. I can recommend the Homewood Suites Garden Grove. It's about 2 miles from the parks, but they have a shuttle. It's across the street from a Super Target which is very handy since they have at least a mini kitchen. They offer free breakfast and evening snacks, and there is a Starbucks in the hotel next door.
Knott's Berry Farm is another theme park about 15 minutes from Disney and it's alot of fun, and much cheaper than Disney.
SeaWorld offers a deal where you buy a day pass for $59 and get a 2nd day free. The zoo also offers package deals for the zoo and Wild Animal Park (about an hour away). Next to the zoo, there is a little railroad and carousel that's alot of fun. Seaport Village is a great tourist spot. Lots of restaurants & shopping on the bay. You can also take the ferry from the embarcadero ( a few blocks from Seaport V.) over to Coronado Island. At the ferry landing you can rent bikes/surreys. On the other side of Coronado, which the Grand Floridian is modeled after. Hotels in San Diego can get very pricey, especially in summer. My sister was there for a wedding this summer and was happy at the La Jolla Beach TravelLodge. It's just a couple of blocks from the beach. It was about $90/nt in summer. Mission Beach is very popular. There is a roller coaster, arcade and indoor pool there, and it's right across from Mission Bay, if you want to play in the water without the waves.
LegoLand would also be awesome for your DD. It's about an hour north of San Diego. It really caters to kids about 9 and under. They have a water play area, so bring a swimsuit and towel for DD.
I hope you have a great trip!