OK, the Anaheim is great for a base, but I think splitting up the trip is a good idea, and not staying in San Clemente.
There are plenty of different types and styles of Hotels/Motels in the Anaheim/Garden Grove area with decent pricing due to the competition.
Also, there is plenty to do other than Disneyland (a typical visitors spend 3 days just at the Disneyland Resort (2 different Theme Parks) in the area, such as Knott's berry Farm, Three Different Dinner Shows, Museums, Major Sports venues, lots of great shopping, and if you want to visit a beach, lots to choose from with a reasonable drive. Here is a link to what is offered in the area.
If you are interested in LEGOLAND in Carlsbad (Northern San Diego County) I would plan to do that driving between the two cities, leave early from one, spend the day at LEGOLAND and then arrive at the other in the evening.
As for San Diego, of course, SeaWorld and the San Diego Zoo are the most well known ones, but there is much more.
I would look at what type of things you would want to do at each area, and then do the split, many folks would go 6 or 7 nights in the Anaheim Area, and the rest in the main part of the city of San Diego.