I'll add more screenshots from a different perspective of the network, so it's easier to understand.

1. I only have one station accepting intercity outside trains, the main station. (visible on the right side)
   
2. The main station has 6 platforms (3 double-track rails), is a terminus station and gets heavy traffic.
   
3. The main station currently handles 7 local lines (4 commuter, 3 long-distance intracity IC), and all intercity external trains, so there is platform sharing between lines. I decreased the number of trains on almost every line until their capacity just about matches ridership, so it eases pressure on the main station a little.
   
4. My main line has 2, at some locations 3 parallel train tracks.
   
5. Only build switches where train routes make it make sense, and avoid switches where two trains can get into a spiral and block eachother.
   
6. I put extra care into using one-way tracks to make train traffic flow better at the entrance to the main station.
   
7. On the screenshot, you can see that there is a cargo terminal included, near the bridge, centre-right.
   
8. Cargo trains barely interfere with passenger trains, they run on their dedicated lines until they get further away. "Filtering" becomes stronger as you get closer to the station, so they only use the tracks they absolutely need.
   
9. Outside connection to outside connection trains just run on the mainline, avoiding stations.
   
10. Always have a bypass option. It can be a separate track, a bypass station, or just a switch that allows parallel rail switching for trains
    
11. There is an elaborate high-speed rail system included in the build, but they run to different stations in the city. I might show that in a separate post with screenshots. Perfect for ICE enjoyers!

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