I think SF like any city is what you make of it. It sounds like you never made that many friends who were native/lifers in SF and you missed out on anything deeper than what you could read in a tourist book.

Cities take time to get to know, and the most important thing is to get to know other people who know the city better than you.

If you had tried biking more in SF, you also would have found more things to do and less to complain about.

Almost all your hate points are worse in NYC IMO.

One last thing, San Francisco is NOT the Pennisula (San Mateo, Palo Alto, etc) and both places are extremely different. Most of the pennisula going down to San Jose is pretty much like Atlanta, Most of Texas or San Diego.