I have never really liked to ask for features in a game, as it would mean more things to do for the devs, but I feel like this game should support at least what has been called P-loops and allow to join the same station twice in a line. Why that?
First of all imagine that you're running a circular line, and a new station appears on an island, next to that line. What to do then? You only have the option to spend two tunnels for joining it to your regular network, or to make it a linear line with the consequent loss of effectivity, which would probably collapse the network because it would most likely need a revamp of the whole map. A P-loop there would be an elegant solution that allows you to maintain your network shape with a bit of planification, if passengers are able to commute with trains of the same line, especially if the crossing station is a non-standard one in the zone, which you currently aren't allowed to repeat.
Another one that happens a lot for example in Auckland is when you find yourself with an station that requires a tunnel because of the bays and water inlets. You can maybe join that station to another one without needing tunnels, then you have to create a tunnel just for a small piece of water that wouldn't be crossed if joined from that other station, saving you a tunnel which you need to use due to the route creation mechanism of the game. In fact, if you wait some time, a new station may appear that allows you to save that tunnel!
This would also allow to join a strange station two (or more) times to a line, at the cost of increasing the length of the lines. It would reduce the frustration of having 10+ circle stations without a single triangle or square, but would need you to be careful enough not to make lines too long to serve the rest of the circles on time.
Probably there will be some ideas I haven't thought of for and against the idea, and don't know about the complication of implementing that, but I'd say it could be a good enhancement for the game.