Well the geography and political climate of San francisco and its surrounding towns make this pretty difficult. It's a small city in a major earthquake zone, with tons of hills, surrounded by water and suburban neighbors who consistently vote down any expansion of the existing rapid transit system. Any new transportation infrastructure would take literally decades (see California's coming high speed rail line).
Only problem is politics. Japan has all that and pulled it off a bit too well. Similar goes for the crazy sandcastlers like Singapore.
I can't blame them (SF-dwellers) they had someting rare in the US for a little time. And general ignorance in, general ignorance out, that's local municipal politics, due to short-term incentives and big "costs" of initiating any kind of change or shift to a longer term horizon, nothing will change fast enough, so a lot of people will get bitten by these problems.
It costs a fuckload of money, sure, but efficient cities are pretty much unimaginable without them (for now at least).