One sees on Railpage a regular complaint along the lines of the government/Premier/some politician should be shot because of some transport issue. Unfortunatly Melbourne's transport problems are not simple and are not going to be solved easily any time soon.
The problem is simple, compared to other metro areas of large cities Melbourne population density is VERY low. Greater London for instance has a population of 8,538,689 (2014) and an area of 1,569 km2, Melbourne on the other hand has a population of 4,529,500 (2015) in an area of 9,990.5 km2, ie London has a population density 12 times that of Melbourne, 5,223/km2 versus 453/km2. What this means is cities like London have VASTLY more funds to spend on transport than Melbourne will ever have.
THERE IS NEVER GOING TO BE A CHEAP AND PAINLESS WAY OUT OF THIS. The obvious solution is to convert the inner metro area where transport infrastructure is excellent into medium density housing, blocks say 10 x 30 to 40 metres containing 4 or 5 story dwellings with a separate unit on each floor, as is done in cities like most London, Paris , Berlin etc .
We will very probably never be able to build really good transport setup for Greater Melbourne for the money everyone is willing to put up.