I agree that the Courtyard Marriott is the nicest "affordable" hotel. The regular Marriott is directly across the street from it. If you have a car, some of the hotels on Embarcadero may be an option (especially if you are able to use a AAA, AARP, or military/govt discount).
Courtyard Marriot
Use Marriot, it's the nice area is good for bistro or specialty dining. I highly suggest secured parking or well lighted street on Telegraph.
There's a variety of hotels within driving distance.
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