Best Transportation / Train Logistics Game?

There’s a new Port Royale coming out imminently, but it’s not really what you’re describing. I’m not sure TF2 is either, to be honest. The maritime aspect is fairly simplistic (basically cargo v passenger, large v small ships and docks). Repair is weird in the game. It doesn’t directly affect operating costs or anything like that, it just affects your pollution stat (which in turn inhibits city growth). So to keep that stat down, you either have to pay more for maintenance or sell your old vehicles.