Are you doing four days total, or four days just at Disneyland? You can't really do the five places you listed in four days, so, I'm assuming it's 4 at DL and one each at the rest.
Buy as many of your tickets as possible in advance, either at AMA or online. It'll save you some money and some time when you get there because it'll be one less line you need to stand in.
As said, there's no real advantage to staying in a Disney hotel. In fact, there are some hotels across Harbor Blvd that are closer to the front gate of the two parks than the Disneyland Hotel or Paradise Pier. The Grand Californian is a really nice hotel that literally overlooks California Adventure, but it's pretty pricey. If you can get a hotel anywhere along Harbor Blvd between Katella and Ball, you can walk to the parks. There's also a shuttle bus that goes to all of the hotels in the area for a small fee. I wouldn't recommend parking at DL unless you get free parking and are staying somewhere without a shuttle.
Go to the Disneyland parks during the week and the crowds should be really light. Saturdays and Sundays will be busier, so I'd go somewhere else on the weekend. If you buy a multi-day ticket, it'll allow you to park-hop between Disneyland and Disney's California Adventure, so picking a park shouldn't be a big issue.
To avoid lines, use the Fastpass system that allows you to get a pass for a ride with a time stamp, then return after the time on the ticket to ride. I don't think any of the rides that would appeal to the pre-school crowd have Fastpasses anymore, so it may not be as valuable to you.
If your older child wants to ride the coasters but the younger doesn't (or isn't big enough), and both you and your wife want to ride the rides as well, ask about a child swap ticket. Basically, it allows you to go through the line as a family, then you ride with the older child while your wife waits with the younger one, then, when you're done riding, your wife rides with the older child while you wait with the younger one.
Overall, crowds probably won't be a big issue since you're going mid-week in early February during a recession.
If you want to start at the back of the park and work your way forward (going opposite from the crowds), hop on the train right when you walk in the gates and ride it around to the ToonTown station. This will drop you off right outside It's a Small World and ToonTown on the north end of the park.
Are you renting a car or will you be taking a bus from Anaheim to San Diego? I'd recommend the rental because it gives you a little more flexibility, and for four people, it'll probably won't be much more expensive.
Personally, I would not do Universal if I were you. There isn't much there for young kids, and not a whole lot for adults either. If you're staying in Anaheim, it's a long drive for not a lot of pay off.
If you are going to have a rental car, I'd also consider the San Diego Wild Animal Park rather than the Zoo. It's quite a distance from San Diego itself, but not much difference if you're doing it as a day trip from Anaheim. It's different from a regular zoo because the animals are in larger enclosures that better simulate their natural habitats. Of course, if you want to see the pandas, you have to go to the Zoo.
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