How do people organise and manage a large passenger network? I build one station per town, and organise bus lines to all converge on this station. Each bus line would be named after the town, with an a,b,c etc added to the end. Then each bus stop would be named after the bus line, with a 1,2,3 etc added. So if the town was Appinghall, I might have a bus stop Appinghall b3 which is the 3rd stop on the second line built in that town. The train station would be named Appinghall station, or whatever name the game gives me (typically Appinghall x station). Then I would have a number of train lines connecting the towns together. I would Identify a small number of rail hubs, connect the hubs together, and add lines radiating from these hubs to each town. I would typically name them after the hub town first, then the town at the far end of the line next. I would also add a mailbox at every bus stop and station, and add postal vehicles to every bus route, and postal carriages on every train.
This worked well in standard simutrans, and with only a smaller number of towns. The network only ever needed to have only one route between any two points as this kept things simpler, and transport time didn't really matter. I'd have a good idea where each town was, and with my naming system if I had a problem with too many passengers somewhere I'd find it quite easy to know where they were trying to go, and which route they were using and would need upgrading. If I saw 400 passengers trying to get from Appinghall station to Appinghall a3 I'd know to add more buses to the Appinghall a bus line. Now I'm running experimental and larger maps with 50 or more towns, and finding that its getting more complicated, and my system is under stress.
With transport times mattering so much, I start to build multiple links between locations. A bus stop may now be on several local routes, and so I might name my stop Appinghall a4 b2 because its on both the a and b routes. Then I start building bus routes from one train station to the station in an adjoining town, with further difficulties for my naming sysytem. I'll name the line for the two towns it joins, and leave the stops on this line with whatever names I'd given them previously, or whatever the game gives them.
With larger number of towns, simply naming the line after the first and last town isn't so useful as I don't have in my head where every town is like I used to with a small number of towns.
With convoy spacing, and overcrowding pressures in pak Britain exp I've gone away from mixing mail and passenger traffic on the same line. I haven't done much work yet on setting up a separate mail network, and have thought of setting up a separate player to run a mail network, but haven't tried it yet.
And how do people like to identify areas of the network that need expansion? Currently I rely mostly on a combination of visual inspection to spot coverage gaps, and responding to end of month messages for stations that are over capacity. In the past I've sorted station and city lists to look for stations with high passenger numbers and cities with slow growth to find problems, but find that station waiting tends to only show major problems, and city growth rates are relatively inconsistent.