Systemwide optimization invariably shows seams in the system. When Switzerland designed the Bahn 2000 network, there was extensive optimization of everything, but at the end of the day, Zurich-Bern was going to be more than an hour, which would not fit any hourly clockface schedule. Thus the Mattstetten-Rohrist line was born, not out of desire to run trains as fast as possible, but because it was necessary for the trains to run at 200 km/h most of the way between Olten and Bern to fit in an hourly takt.
The same is true of speed and capacity improvements. A faster, more reliable system attracts more passengers, and soon enough, a line designed around a train every 15 minutes fills up and requires a train every 10 minutes, 7.5 minutes, 6 minutes, 5 minutes, 4 minutes. An optimized system that minimizes the need for urban tunneling soon generates so much ridership that the tunnels it aimed to avoid become valuable additions to the network.
Electronics before concrete
The secret why swiss transit works so well: the whole schedule is synchronized: