RE: We had a nice room at good priced hotel right off Mission street.
Your biggest mistake, right there. With the exception of a couple blocks near the Embarcadero, that street is nasty.
It is not that is is "nasty" so much as it is vital. Lots of dynamic Hispanis culture, Asian (of several flavors) and some black. It reminded me a lot of Roosevelt Ave. in Queens (NYC) several years back. There were damn few empty shops on Mission and a WHOLE bunch of really interesting looking restaurants.
SFO is a fabulous city. I had lunch at a harborside place. Alas, the politicians are trying to kill the golden goose. Everything is so expensive (except the bus ride - $1.25 one way but you a transfer for a free return trip if it's withing 4(?) hours- the transit people NEVER check) what with minimum wages, taxes and taxes.
All the negatives are true! But, it is still a wonderful place to be.
Yeah, at night it was. But it was convienient for getting around doing the tourist stuff. It was the Best Western...the pink one on 5th or 6th. Nice little place.