It's cleaner than anything in Silicon Valley and less crowded than NYC. Timeliness and reliability are quite lacking though. It desperately needs rolling stock that wasn't due to be EoL'd a decade ago and it needs proper management which the thinly veiled jobs program known as the MBTA doesn't seem to be able to provide.

edit: apparently SF is not representative of public transit in other cities in California.

DC Metro is having issues on par with NYC's. The cause is likely the same; improper maintenance.