if your train lines are getting clogged up then you need to separate your internal train network from the external train network. i now usually have one station which is dual track, with one of the lines being external connections only and the rest internal. i also keep my industrial lines separate, there's a very useful dual track industrial station in the workshop too, it's much harder to keep industrial network free of jams but it's possible with some tweaking, i make sure most of the industrial lines are underground so the utter chaotic mess that it is can't be seen. the train lines never get clogged any more.
if you use dual track stations, be mindful that external lines never use one of the lines, so if you no longer get any external traffic switch the external line to the other track.
They sometimes get clogged anyway even when separated. It's the way CO setup railroads in the first place. When this was first mentioned, this was one of the first things I did and it does help to a certain extent. I discovered that issue with the stations ages ago. It's too bad because it means using more real estate for railroads. So for these locations where I want passengers to switch lines, I have two stations back to back, as best as can be allowed with a footbridge between the two stations. For the most part this setup is successful.
However, like the rest of the traffic system, it's very broken. Instead of railroads running a fixed amount of rolling stock on a fixed system, their simulation keeps adding rolling stock because the system is treated like roadways with automobiles.
Why would a train run with only one passenger?
It's a waste of track space and a waste of resources.
Why keep filling the line with more and more trains?
Sure we can use the public transport mods to cut back on the number of trains, but shouldn't this logic be built-in?
Why are trains, passenger more so than freight, not run on specific schedules?
We should be able to setup schedules for passenger services. A commuter rush hour where we can specify more trains at specific hours with an hourly service in the day in between the setup.
Why are there no headways setup?
Because of the fixed system with limited space, trains need to be timed so that they don't bunch up. Yes, BloodyPenguin's (I think that's who it is) has an extended PT mod which does add this in, but it should be built into the system and be more effective. Bunching causes the clogging.
Why no signaling capabilities?
This is a big problem in the simulation. Signals are used to not only prevent collisions at junctions, they are also used to control the flow of traffic on the line. On a single track line with no signal system, a single train can run unhindered in either direction. Using block signals to separate the track length into multiple sections, allows multiple trains to traverse the same line and are kept apart from each other by moving one train from one block to another. Lines are also controlled with signal boxes, which can divide up the line into blocks that are manually switched. Today this has pretty much given way to a mechanized system with dispatchers located 1000s of km from the track its self.
With double-track and passing loops (sidings) on single track, trains can run in both directions on the same track. This setup too is also governed by some kind of control system. In the US and many other places in the world, there are signals and warrants. in the UK and former Colonies, there are is a token system which is controlled by the train driver. He takes a token from a signal box at one end and because he's the only one with the token, the line is not released until he reaches the other end and places the token (key) in a box.
These are the missing things that cause the passenger railroad system to clog up. No matter how much we try with separate freights and separate outside connections, they still get stuck .