Trains in California suck because of government dysfunction across all levels. At the municipal level, you can't build shit because every city is actually an agglomeration of hundreds of tiny municipalities that all squabble with each other. At the regional level, you get NIMBYism that doesn't want silly things like trains knocking down property values... And these people have a voice, because democracy I guess (despite there being a far larger group of people that would love to have trains). At the state level, you have complete funding mismanagement and project management malfeasance that makes projects both incredibly expensive and developed with no forethought whatsoever (Caltrain has how many at-grade crossings, again?).

This isn't a train problem, it's a problem with your piss-poor government. At least crime is down, right?