We had a great time in San Diego on a brief stop over before heading to Anaheim. A couple things to be wary of:
1) The parking garage costs $25 / day and is really tight. Wouldn't want a large SUV.
2) Wifi is not free. For 3 nights that we were mostly gone it wasn't a big deal, but if you are planning on spending time in your room it's annoying.
3) The pool was really small. Like tiny. If more than 6 people are in it, there is really no swimming possible.
Other than that, we really enjoyed our time. Clean, full kitchens, free laundry, and close to a lot of the sights: 10 minutes from the airport, 10 minutes to the zoo, 10 minutes to the port, and 20 minutes to Sea World.