Agree with some of the points made above.
With regards to resignalling for closer headways watch this space and the Dandenong corridor specifically.
Melbourne is stuck with large numbers of level crossings on some lines and which cannot be grade separated in many cases. However many are only modestly used so there could be a program of consolidation whereby two of three close crossings remain open but an intermediate one is closed. That would go some way to ameliorating the effect of close-headway trains upon road traffic.
To have country trains running via Upfield would require dual-gauging of that route. Far better as things stand now to have those trains run via the RRL and the Jacana Loop though at the cost of not being able to serve the likes of Essendon. While some are on the broad gauge now that may not always be the case as standard slowly gains ground outside the metropolitan area.
Dual-gauging Upfield will require relocation of the stabling facility there and will require some significant grade separation works at Somerton. As things are the ARTC appear to be insistent that any such works are to double-stack clearance despite the improbability of double-stackers reaching Melbourne while Bunbury Street tunnel exists. It will also have an effect upon line speed placing more restriction on country trains than on suburban sparks but in total will affect the route capacity. More trains on the Upfield line are constantly demanded; it does not meet Metro's aim for a 10-minute daytime headway and cannot do so while the single track remains north of Gowrie and while there is insufficient capacity through the City Loop for those additional trains. Having them turn back short of Flinders Street is unlikely to be a popular option with users but might be workable operationally.
We are, I am afraid, stuck with a substantial fleet of Xcrap trains for many years to come. All types in the fleet have their faults and weaknesses. The next sizeable rolling stock order may be to start Comeng replacement in perhaps 5 - 10 years from now.
In general I welcome the move to a "metro-style" service with daytime headways close enough that a timetable is not needed. What Metro should remember however is that just like London some lines are rather long with end-to-end travel times above an hour to the City. Few journeys on the London Underground take that long. More express running and significant cuts to travel times will make the service more attractive. I know of many people who will not consider the train from Frankston to the City because it takes around 65 minutes and feels very slow. Driving can take as little as 30 minutes, typically 45, and doesn't stop at 30 intermediate stations. Free unrestricted parking is also impossible at or within comfortable walking distance of Frankston station after 6.30am.
Yes more needs to be done as a whole package. There are encouraging signs that this is being addressed. Rome wasn't built in a day and neither was Melbourne's public transport system brought up to scratch. But it's headed in the right direction and not before time.