I live in Carlsbad so I agree with 1 day each for the Wild Animal Park and the zoo. The hours of both parks outside of summer are rather short and figuring in the drive between each you are bound to not get to see everything you want to.

I don't really think you need 3 days for the Disneyland Resort anyhow. 1 day each for Disneyland and for California Adventure is fine. I actually did both Disney parks in 1 day but that was with no kids.

I'm meh on Legoland but then again I don't have kids.

Sea World is a fantastic option too. If you go there though wait to see the Shamu show at the end of the day after dark. Seeing it during the day time you miss out on all the cool lighting effects.

If your son is anything at all like my nephew who is nearing on 6 himself, he's nuts about animals. He already knows all of the exhibits at both the San Diego Zoo as well as the Wild Animal Park and he hasn't even been out to visit me here yet.