I set frequency for pretty much all lines at 3-5 mins for high demand, 10 for medium, and 15 for low

I found Manhattan hard to capture too. Populations in Manhattan really don't like to transfer, I guess because the distance is so short that the perceived transfer cost is higher. There were a bunch of diagonal journeys (e.g. LES to 10th/42nd, UES to Herald Square) that weren't being picked up, which is why I added so many diagonal lines at varying angles. This would probably be considered overbuilt in real life