Andrew Lezala is right. Train timetables are too complicated. We have express trains running direct between Box hill and Richmond. Some stopping at Camberwell and Glenferrie. Some stopping at Surrey hills, Camberwell and Glenferrie. No wonder it's confusing for patrons and controllers!
I think the simplest solution is to have two services only. One express service stopping at premium stations only, and one stopping all stations, running a nominal 5 minutes apart (less during peak periods).
So if you miss a train you know the next one will be at most 10 minutes away, 5 minutes if you're willing to stop all stations.