I picked the area with a highway crossroads with some plains surrounded by forest with a river and lake. That highway is the biggest issue. It split my town up, and I couldn't seem to just build road going over the highway with overpasses, so every time I had to cross them, it'd create a new intersection that led to traffic backing up horribly on the highway. I had to make sure every area of town had at least its own schools, fire station, clinic/hospital, and police station.
I never quite figured out the bus system, so I think my town's bus routes are about as chaotic as the all-too-real bus system in the city I live in. I think the subways will help, but they're not cheap.
I feel like I'm spending all my money building new roads and basic services for new districts to expand the city, and can't afford to build some of the more advanced buildings.
Also, I could be wrong, but given the way the river is starting to look downstream of the sewage pipes, I think building a dam anywhere in the area would probably lead to some kind of environmental breakdown that will poison the people of my city worse than Flint, MI. I'm already concerned about how the industrial district seems to be creating a barren area around it... trying to make sure further industry is separated from the rest of town, but that's not terribly realistic, nor is it easy to do with traffic and all. Adding bus lines and a metro station would probably help with that, and maybe a six-lane road...
So many lessons to learn on the fly!
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Ach. You're right. The "good" ending (spoilers in the video) still ends up with the Institute destroyed. Garvey's comments on that are kind of gold, though.