On our trip we stayed at Parc 55. Wyndhams location in Downtown Sanfrancisco, it is a spectacular property with fabulous rooms, and views. We ended up with spectacular pricing over the busy holiday season (only didn't have Christmas in the itinerary), that made the trip very affordable. It was so well located for the trip too, Union Square is the center of many of San Francisco's Transit Lines, and with a large number of shopping centers and streets nearby there was always something for everyone to do.
The restaurant located within (CityHouse) was also fantastic with great service.