A really nice motel in San Francisco is the Columbus Motor Inn on Columbus, away from the hustle of Union Square but near Fisherman's Wharf and central to Little Italy.
Positives: nice rooms; it's a pretty safe place to walk around at night; free self parking; relatively quiet(unlike Union Square); plenty of pubs, Italian food and Gelato places close by.
Cons: no free breakfast; no sweeping panoramic views from the 24th floor.
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