I still say stay in Mission Hills for accessibility. If we have a rainy Christmas week, the beach areas tend to flood down by South Mission and PB. Getting a rental at Mission Hills sounds the most economical and most central. If you get a chance, drive by El Indio on (India Street) and try their Mexican fare. You can also visit Little Italy and sample the environment at Filippi’s Pizza (also on India Street near the airport). There is limited parking so try to go during the week for lunch. Evenings are crazy in that area. The kids will love it! You enter a “storefront” and pass through an Italian Deli (all original, maybe 1950’s era?) to get to the restaurant in the back. Service is fast and food is hot. Check out the messages on all of the old hanging wine carafes.
India street can get confusing because it was divided by freeways in the 1950’s, so you need to know that is it a long, really long, sometimes, one-way street. Ask and pre google map everything.
The Organ Pavilion publishes its schedule online but right now, it may be too early: http://spreckelsorgan.org/
The Balboa Park area is beautifully decorated for Christmas.
I second the Rubios Fish tacos and the Roberto’s/Alberto’s visits. For real Barrio food- Las Cuatro Milpas, bring Cash, “dey no take credeet cards”. (Near the Coronado Bridge exit/entrance.) It is the Barrio, so wait in line and sample the family food there on picnic benches. It doesn’t look good, but delicious and famous. Only open for lunch, but great Tamales!
In OB and downtown, I haven’t been in a while but HODAD’s for burgers. Google them. The OB location is a must see.
Take the kids on the Bahia Belle; it is decorated for Christmas and goes from Bayfront hotel to Bayfront hotel: http://www.bahiahotel.com/dining-entertainment/bahia-belle-boat-cruise/
Have fun!