...or when (like the weekend of the first AngelHack event) you are delayed because your train hits a pedestrian (a horrendous sound by the way - you know exactly what's just happened immediately) then the replacement train is delayed because the next train in front hit a second pedestrian. They need to sort out the grade separation, it's just ridiculous, not to mention tragic.

Totally agree.I wonder why Caltrain is inefficient at times.

What prevents Caltrain to do better in terms of keeping up with schedule? Also, there must be a way to keep fare reasonably cheaper than cost of driving a car to work.

It's a lack of willingness to invest in the infrastructure. Which is a chicken/egg thing - legislators won't vote for investment as voters don't support something that doesn't deliver value.