If you are going to do Chicago there are several options you might consider. One is to include RTA's Metra Commuter Rail Trains as part of the rail network. While fares issues have kept system integration slow, eventually, better route and fare payment options will be available.
The second option to consider is to use the routes and stations that were available around 1900 when the Chicago Rail system was much more robust, more lines and more stations. I'm not sure to what degree your software allows the addition of new stations as I found it today, such as one at the end of the Green Line at the Museum of Science and Industry (4 Million Visitors Annually), but that would be an interesting feature as well.
Am just about to buy your software on Steam. Good luck.
Peter James Foote
Former Transportation Research Board Committee member, now retired.