We stay at the Marriott Marquis, I believe it is on 4th and Mission. The hotel has so many room types, the upgrade possibilities are endless. You are 1/2 block from BART and MUNI, so you can get anywhere in the city very easily. You are also across the street from Yerba Buena gardens, the museum of modern art, the Metreon, etc. We live in the Bay Area and come here just to hang in the city. Across the street you will find two movie theaters, a kids park, etc. The City Center, the shopping epicenter is accross the street, so is the Old Navy Flag ship store. Union square, the Embarcaderro and Ferry Building Farmers Markets are just a short walk. We just stayed there again over the 4ht of July weekend.
Check out some of the B & B 's in the area expecially west of Embarcadero. Several properties including some castles were renovated and converted to B & B's. We stayed in one over 5 years ago where each room was decorated from the Victorian era and named appropriately. Don't remember the name or I would provide it.
You basically you have 5 good options in the Downtown area of San Francisco to consider. I stayed in all of the Hotels each has it's own benefits, I think the San Francisco Marriott Marquis could be the right choice. They are all centrally located with easy access to the entire city. San Francisco Marriott Marquis – Near major Museums, Moscone Conference Center, 1 - 2 blocks from all major shops; Union Square. Great insight Pool, nice views of the City from upper floors. JW Marriott San Francisco Union Square - Nice property, 1 block from Union Square, near major Theaters, some of the nearby neighboring streets are not the most desirable areas of the city. The Stanford Court Renaissance San Francisco Hotel - Nice place with old City Character, near Union Square, uphill walk to the Hotel. Near two Trolleys routes and stops. San Francisco Marriott Fisherman's Wharf – In major tourist area, middle of Pier 39, SF Bay, Golden Gate Bridge; good for kids, near two Trolley routes and stops. San Francisco Marriott Union Square – Newest addition to Marriott, 1 block from Union Square, all shopping, good place. Near two Trolley routes and stops by the bay.
I'm a huge fan of the Stanford Court. If you get one of the "big" kings along the side - they have tons of space, updated features and are quiet. The restaurant is delicious and the staff is terrific. It's a quick walk/cab down to the city, but not tough at all.
I like to stay at t he Courtyard San Francisco Fisherman's Wharf. There is nothing fancy about the place but it has very easy access to the cable car, trolley, and the Columbus Avenue bus. So, from just a block or two from the hotel you can easily get to any other part of the city. If you hate the wharf stuff you don't have to ever go down there - it is a block or two away. There is also another Marriott a few blocks down on Columbus. I always try to stay at the Courtyard San Francisco Fisherman's Wharf when I'm in town, but I'm real big on low-key convenience.