Just noticed this when looking at bus timetables for Melbourne Airport tonight.
Commencing on 26 Sep 2010, there will new frequent smartbus service 901 that runs from MEL to Frankston via Broadmeadows station, Epping, Greensborough, Doncaster, Blackburn, Ringwood, Knox and Dandenong.
Frequencies vary, weekdays from 6am-9pm runs every 15mins, other times more or less every 30mins. Runs from around 5 am to midnight on weekdays/Sat and 6:30am-9pm on weekends.
Now whilst the whole journey will take between 3.5 and 4 hours, its only 18 mins to Broady station. That would make the trip to Flinders St somewhere between 55 and 75 mins, depending on wait at the station. Skybus still a lot more convenient, but at least now there is a practical public transport alternative, at least during daytime.