I ride Caltrain every day and the experience annoys me a lot (still less than driving), but I feel sorry for the people running Caltrain because despite providing a valuable infrastructure service that is in huge demand, they are considered the lowest priority by everyone they interact with and have to deal with the most ridiculous restrictions and regulations. For example, Caltrain knows that they are always behind schedule during rush hour and want to adjust their schedule. But to do that they have to consult everyone and their uncle over a year-long process where every nutjob's concerns about a five minute scheduling change can stall the entire process.
Infrastructure projects deal with such problems everywhere, but I have not seen a place where this attitude is so deeply engrained and systematic like here.