Thanks for the response!
I'll check out the JGR patchpack (if I can find it). The timetabling took a time to really understand, but I've noticed that you can't do very much with it. Luckily trains overtaking each other isn't happening that much anymore (It used happen all the time due ineffective depot placement, causing trains to pass stations and having to wait before they can drive back to the station). The waiting times have been tightened here and there, after I learned that with some tweaking you can change NewGRF's ingame. There were warning everywhere that OpenTTD might crash or behave in unexpected, but I have yet to notice anything. Since I decreased the loading times, some lines have had improvements in their waiting times, which also improved throughput. As for the breakdowns, I'd like to have them present for a little bit of randomness, but it would be nice if it happened a little less
At the time of writing, I've implemented a few changes to the network:
A few sections have been upgraded to four tracks around Fonborough, Gonburg and Fundinghattan. The Chefingway station was moved south, and some lines changed. A new line from Fundinghattan to Gonburg via Fonborough was added as an extension to an existing line starting in Gonburg. There's a new train from Honninghall to Fundinghattan via Prardham, which is now a transfer-like station if passengers were to go from Chefingway to Fundinghattan.
I've also worked on the situation around Gunnpool, Bahattan Springs and Prenhattan, which is now four tracks, the stations have had a make over, and the trains drive at 15-day frequencies.
I'll consider adding an extra direct train from Honninghall to Fonborough, although I'm not sure it's necessary at this point, since the upgrades have turned the Cargodist lines to green again
Addressing another point, you were talking about a direct connection between Honninghall - Fonborough - Trutburg. Is was already considering to move the high speed tracks away from Trutburg, and instead connect them to Fonston, where it seems a lot of passengers try to go via Flufingway Heights. By rerouting the high speed tracks, it may relieve the trains from Fonston to Hartown.
As for the network design, I understand the approach of dedicated tracks for different lines. I'm however not a big fan of it. I used to just let the trains pick a platform. When it became a bit crowded, I tried using waypoints to force platforms for each line. This only created the problem that it became very hard for delayed trains to overtake other trains, so I stepped away from that approach. What I'm trying now is a sort of many-to-many-to-many approach, in which a train can be on any incoming track, is able to enter any platform available, and is able to leave from any platform to any outgoing track. This has however the downside that it's quite complex to implement without tracks crossing each other, which makes me wonder what's next. I have started looking around to real life examples where different lines meet, such as Den Haag Centraal,, where three lines come together at a terminal station. What I've noticed is that each line has a few of the platforms they can go to, while sharing some with the line next to them. In another game, I've tried implementing this, and it seems to be way less design intense, while maintaining a rather good efficiency, so I might combine the two ideas in the future, and perhaps it's the next big thing
In the beginning, I did run freight trains and passenger trains together on the same track. As I've set almost all costs to their highest defaults (And I've started other games using a base cost mod multiplier), it was quite hard to break even. But since the network was quite small an innocent back then, it wasn't that hard to tune the timetables for everything to work out just fine. As games progress however, I usually drop the freight trains in favour of passenger trains
I'll post a few screenshots of improvements I have implemented so far when I'm back home tonight!
Thanks for the advice!
*EDIT: Added a few screenshots