I'm not sure I would go to the zoo just to see the Pandas. The last time I was there (several years ago) you had to wait in line to see them and sort of walk through. They don't rush you through but you can't just stand there all day looking at them like you could any of the other animals. I think they also had certain times that the panda exhibit was open. It was fun seeing them but I wouldn't just go for that. I'm not sure about how crowded the zoo or SW would be on a sunday.
If you don't want to do another theme park there are lots of other things to do in SD. There is Old Town which has some good restaurants and little shops. There is also the USS Midway aircraft carrier you can tour. DH and I did that last year and thought it was really interesting. We aren't especially interested in airplanes or military stuff but we still thought it was interesting and fun. There is also Balboa Park (that's where the zoo is). They have some museums there and also some gardens. You can also take a boat tour around the harbor area. Those are just some ideas off the top of my head.
It's hard to say what the weather will be in October since it's sort a transition period but SD does stay cooler than places more inland (like Anaheim). If you want to go to the beach in swim suits and play in the ocean then it probably will be too cold. Actually, the water off the coast of California is always cold so I personally don't enjoy swimming in it even in the middle of summer but a lot of people do. Even if the water is cold and the weather is chilly, you can still go to the beach and enjoy it but you need to think of it differently. You don't go in swim suits, you go in jeans and a jacket. Instead of sitting on the beach getting some sun, you take a walk and watch the waves and look for interesting things that wash up on shore. Not many shells on california beaches but there are a few. Your kids could still run around on the beach or draw and write things in the sand with a stick, stuff like that. And of course, even when it's cold you can still take your shoes off and dip your feet in the ocean for a little bit.
Hope that helps a little!
