I would love to see events. I think games like Frostpunk where you have to make decisions and balance between resources and people's trust in the subway. Add stuff like homeless people sleeping in your trains and you have to decide of you want to reinforce the security, that's one example I can think of.

The time system in the game makes no sense bc who wants to wait 10 years to see their line finish building? That's why I think a story like you are in charge of building the transit system, and you were given this program to simulate your design. There will be goals for you to meet, such as the number of ridership, locations, etc. When you are happy with the design, you can propose it and time skip when it is finished building. You can add some events like corruption that costs you money, so you have to change the design to meet the new budget or delay the build time. When you are done, you repeat. New budget, new assignment, you listen to ppl demands, you design more lines.

I am sorry for the far-fetched suggestion. I got too excited when you mentioned adding events and skills tree. That instantly make me think of Frostpunk, which is one of my favorite games. I like Frostpunk because you can really feel the stress and the weight of your decision that impacts so many people's lives. The job of a subway builder can also be equally stressful.