There was a similar thread some time ago discussing the merits of quad between Dandenong and Caulfield. I have been unable to find the post I was looking for. But I digress, the general thrust was more time saving could be made in the 200+kms after Pakenham than the 58km to Flinders Street. Some smarty with the calculator worked out that something in the realm of an hour could be shaved off the running time with improvements to curves and track speed. Far out weighing the 20 or so minutes that could be saved between Dandenong and Flinders Street.
I do agree the current situation is a bit of a mess. It is no comparison to the mess RRL fixed only to create new ones. One of the biggest problems we have currently in Victoria, partly thanks to Dan, is our obsession with massive projects. We need to squeeze the current infrastructure before we go off spending billions quading to save 15 minutes. With the introduction of Turn up and Go, services on the Dandenong corridor will be fixed. Running time between Pakenham and South Yarra will be fixed. Dandenong to Toorak Road is 26km, this isn't a great distance. If running time can be pushed closer to 30 minutes between Dandenong and FFS this would not be much different to Bendigo commuters. (Sunbury - SSS)
Easiest way to fix the current situation is to upgrade, as much as possible, the track to Class 1. This would allow for 160km/h running for the majority of the line, sliming the current run time down as much as possible.
Also, introduce a 2 tier service as has been suggested. Bairnsdale/Traralgon services express from Warragul to Dandenong, Dandenong too Caulfield. Services every 30 minutes during the peak. 'Commuter Service' from Warragul picking up those not so small hamlets on the way to Dandenong, again every 30 minutes during the peak. Then back to hourly or 40 minutes off peak.
High Capacity signalling allows for theoretical output of 36 TPH. If services departed every 10 from Pakenham & Cranbourne this is 24 TPH, four from V/line is 28TPH. Still have 4 or so spare train paths during the peak period.
We are not yet at the stage of needing to spend billions on quading, the current line is not yet at saturation and won't be from some time. What many have overstated here is running time and people won't use it because it takes too long. This is not the determining factor for many commuters. Reliability is, knowing that if I get on a 0600 train I will reach my destination at the same time everyday.