A couple of things that I have learnt about trains recently suprised me.
My sister visited and was catching the train back to Geelong. I casually asked how much the fare was. About $10 she said. Hmm, seemed a lot, but I did not think much about it until later. I have checked and the return trip is over $20 and takes around 55 minutes each way.
Yet, if you travel in the other direction, that is to Pakenham, a trip that is over one hour, it can in theory only cost $7.10 for a return ticket.
I doubt that the suburban system is privately run and the Geelong service is government run has much to do with it. It is probably more historical.
If I was a Geelong resident, I would be protesting.
A workmate was rushing for a train on the Pakenham line. He told me if he missed it, it would be an hours wait for the next one. It was not even 8.30 on a weeknight. Can't be right. But I just checked Connex timetables and sure enough. If you live beyone Dandenong, the service interval is sixty minutes after the 8pm trains departs Flinders Street Station. It will take a passenger 1 hour 15 mins to get home to Pakenham whereas the Geelong trip will only take an hour.
Maybe that is why it costs so much more.
PS The above info makes no allowance for discounted tickets or express trains.