I like the current game very much, but understandably there are many flaws and things missing being their first game. In the suggestions fixes tab there are also many good ideas. It would be way easier to build a flying junction if the tunnel mouth and slope would be able to have straight walls. This would also make mountain railways more aesthetic by making steeper cuttings or building elevated railways in cities. On the other hand bridge pillars should be able to be place more dynamic so you can cross other infrastructure easier or build elevated metro systems.
Another thing that would be fun to have is the fact that the railway signals, rail track gauge and electrification have their own specifications, so you will have to replace the older ones in time to have greater capacity, safety or the highest allowed speed. So you will have to change to light signals and cab centered controls in time. Coming to safety, the options of trains failing and stuff like that would be fun and so be able to change the maintenance budget to optimize this. With other transport company’s like in OTTD you would also have to change these if you want to make you’re newly bought railways inter operable. Or build trams and metro systems that will be cheaper by having other specifications.
Also the station building should be revised. Building platforms should be done by draging platforms next to rails and afterwords ‘upgrading’ the platforms by deciding how to put the platform roofing. That way you can do simple changes to the station without having to demolish the whole station. If you really want to have a special station, like liege ore something, you could have some restrictions like the platforms have to be straight for a certain distance. Also having 2 exits will be more easy and you can have 2 different kind of exits. You can keep the old exit on one side have the majestic entrance and adding a more modern exit on the other side so they look more like stations do nowadays. I do think thought it is important to have the ability to building the stations from 3 different approaches, either by first building the track, the platform or the station main entrance. I also think that there should be an interface to build underground stations so you can put railways underground or built metro systems with other specs as mentioned above.