We've stayed at the Royal Pacific Motor Inn in San Francisco a couple of times. It's basically a motel. Parking is free. I don't remember if it had free breakfast, but there are so many interesting places nearby to get breakfast. Just a few building down the street is a Chinese bakery, and across the street is Little Italy, where they have many cafes that serve breakfast. The motel is located on Broadway. The motel side of Broadway is the north edge of Chinatown, and across the street is the south edge of Little Italy. The walk to the Bart station is quite a hike, but it's all downhill, you can take the bus back to the motel. Check out Royal Pacific on Google. We really enjoyed staying there, but there were a couple of things you might want to consider about this motel. The motel building is an L shape and the street side gets a lot of traffic noise. In the mornings there are delivery trucks and garbage trucks that are really loud. Also, there is no air conditioning. It's really not needed, except one year we went, there was a heat wave in October and was really warm in the room.
I hope you enjoy your trip to San Francisco!