Well done on a great game, it's quite an interesting concept! I'm not sure if you're familiar with Mini Metro but this reminded me of that a little.
I agree with feedback about easing the player in a bit more, maybe a second tutorial/warmup level that is smaller than the main maps? I got used to the mechanics fairly quickly but going out of the tutorial to a big map was a bit overwhelming at first xD
I don't think the stations changing colour/position is mentioned and I was having a little trouble noticing where the new stations were some times (might just be me, though). Having an in-game pause (Esc to open the menu does effectively pause) to be able to change switches would make managing the trains easier - this may be an intended mechanic to add to the challenge, though.
The artwork is really nice and while I started by using an angled camera, I found the top-down much easier to track the trains - I didn't see much of the art/models this way, though. Personally I feel like this game could easily work as a more 2D/top-down focused game with more station, waiting passenger, switch and track information possible that way. The music too is very calming and nice to have on in the background.
I think the only 'bug' I saw was one train catching up to another and phasing through its carriages, but might have been a one-off?
There isn't any penalty to leaving passengers waiting as I understand it, although managing train pathing/collisions is maybe already tricky enough, hehe.
Maybe too much detail from me, but again overall a great game, very well done to everyone.