I am travelling to San Diego in April with 4 year old twins and did some research in case it helps. I am also planning 6 day stay with all the kid friendly attractions. I have not stayed in any properties but did look at tripadvisor and flyertalker reviews to base my decision.
I decided to use 5 night stay at Sheraton Suites for 28,000 points. I chose this property over the others because it was a suite which allows me to put the 2 kids in the sofa bed and at least have a quiet area for the adults so we dont all have to go to sleep at the same time. The other hotels downtown are all one room unless you get a suite (I am only gold, so likely will not get suite upgrade for 5 days). While downtown, I plan to take advantage of San Diego zoo, Seaworld, USS midway, old town, La Jolla. I admit the other hotels look newer and seem to be a bit better location (only seems to be a difference in 5-10 min walk since they are all downtown) but for a one bedroom and 7000 vs 10,000 points, I thought it was worth it.
Upon checkout on 6th day, plan to go directly to Legoland in AM, stay all day and stay one night at Sheraton Carlsbad @ Legoland. Plan to hopefully get late checkout and play at Legoland 2nd day before heading on to LA.
Total SPG points 38,000 for 7 days, 6 nights. Hope that helps. I will send you a trip report when I return end of April. FYI, I found Costco.com has Zoo, Safari Park and Seaworld combo tickets for 99.00 and Legoland.com has 5 days for the price of 1 or buy 3 memberships, get 1 free on website now.
Also, if you have to choose between zoo and safari park, I heard the zoo is more appropriate for toddlers as the safari park is a lot of walking for the little ones and it is tougher for the little ones to see things since the safari park is so big.