I would not do Universal with a 5 year old and 2 year old. Unlike Disney where so much is perfect for young kids, a lot at Universal is geared towards older kids. Plus, you are talking about a 3 hour drive from San Diego. If the 5 year old is a big dinosaur fan, you can ride train at Disneyland (the part between the Tomorrowland and Main Street stations specifically). FYI---- while the Jurassic World ride had not yet opened last month when we were at universal, I'm pretty sure that ride is about the dinosaurs attacking you and you escaping (its a thrill ride), while at DLR the train takes you past dinosaurs that are not coming at you and the 2 year old can go too. My DD would have hated Universal at age 5-- she would have been scared of a lot of the things there. Universal is still about an hour away from Disneyland assuming there is no traffic.
I would do more than one day at Disneyland if at all possible, especially since you are going at the most crowded time of the year which means it will take more time to get things done. Sounds like you may be planning on going the week before Christmas? I think if you are there the week of the 16th, the crowds won't be too bad yet those weekdays as that should be before most schools get out. I would try to go to the Disney parks before Saturday December 21st if at all possible. I would stay at one of the hotels near Disney, get park hoppers so you can go to both parks, and do both those days in Disney parks. There is so much for the kids to do there- even for the 2 year old. To give you an idea, we typically spend 5 days in the parks at Disneyland
Disneyland has the traditional fast pass system where you can book at the kiosks--not FP+. HOWEVER, Disneyland also has Max Pass. It costs $15 per day per person, but we find it worth it. You get all your Photopass photos with it, including also the ride and restaurant photos. The minute you scan your ticket and walk in either park, you can book a FP from your phone in either park. It still goes by the traditional system where you have to use it or wait a certain amount of time before getting another, but the wait time is slightly shorter on max pass, and also it is extremely easy to book your next FP. I would think it would be worth it with the photos included. Plus, your 2 year old is free admission and don't need a FP to go with you in the FP line, so you would not have to pay for it for the 2 year old.
Legoland would probably be pretty fun for the kids, but boring for the adults. It has been years since we were there, but we were a one and done there. DD was 4 and she really enjoyed it. We found that unlike Disney where they find a way to make it entertaining for the adults too, that Legoland was really geared just for the littles. Although DD really enjoyed it at age 4 (DH did not) , after that trip we would give her the choice between 5 days in Disneyland/CA or 4 days at there and 1 day at Legoland, and the extra day at Disney won every time.
We love the San Diego zoo and another great place is the San Diego Safari Park. We actually enjoy the Safari Park more than the zoo, but they are both great. We haven't been to SeaWorld in San Diego (or if we have I don't remember) because we have been to Sea Worlds in other places.
