Actually, the Japanese shinkansen system long ago provided the solution. Three different speeds of trains. Super expresses that stop only in the main cities, medium speed trains that stop at moderate intervals, and locals that stop at every station. All the schedules coordinate so there is not much more than 5 or 10 minutes or so to wait between different train classes if they both stop at the same station, and usually switching from one to another only requires walking to the other side of the same platform.
If you travel shinkansen by the slower trains, you will often find yourself waiting at the side platform of the local stations a minute or so longer, while the faster train overtakes you without stopping. The local then takes the "slot" behind that train on the same track.
It all works beautifully.
In practice you take the fastest train for the bulk of your journey, then hop over to a medium or local for the last portion, if you are going somewhere more out of the way.
Play around with some destinations here, and you will see how it works. Eg, Tokyo- Maibara (one stop before Kyoto)
If you travel shinkansen by the slower trains, you will often find yourself waiting at the side platform of the local stations a minute or so longer, while the faster train overtakes you without stopping. The local then takes the "slot" behind that train on the same track.
It all works beautifully.
In practice you take the fastest train for the bulk of your journey, then hop over to a medium or local for the last portion, if you are going somewhere more out of the way.
Play around with some destinations here, and you will see how it works. Eg, Tokyo- Maibara (one stop before Kyoto)
Nozomi=Fastest
Hikari=Medium
Kodam=Slowest
http://www.hyperdia.com/classic_en/hyperWeb.cgi