Unfortunately, it isn't that simple.

I have noticed on my commutes that there are times that I simply can't arrive at work. If I'm commuting at an unpopular time, it takes 15 minutes. If I commute at a popular time, it takes 20 minutes. This makes me either 5 minutes early or 5 minutes late, depending on the time I expect to arrive.

The reason the trains take a different amount of time is because when the trains are crowded, it takes a long time for people to get on and off, so the train has to sit in the station longer. This delays the train behind, and so on. A new signal system or better tracks isn't going to fix this problem. It's the human factor of "I want to arrive exactly at 9am, 9:01am isn't acceptable" that's slowing everyone down.