On the whole it's an improvement as it is both diagrammatic (easy to read) and systematic (shows the routes trains actually take) so while not showing the fare zones these can be overlaid as London does very effectively if it were required. London also copes perfectly well with overlaps as has Melbourne with previous versions.
One risk is placing too much information in one place. There may never be a perfect map but the function of a map is fundamentally geographic rather than encyclopaedic. It's probably OK to overlay zones in light type / background shading but not to also attempt to include any more information such as service headways, stopping patterns or onward connections on a map of this sort.
Again comparing with the London tube map that does not show such things but there are line diagrams which do. Their trains are for the most part captive to a single line where ours are not but there is nothing to stop line diagrams with onward connecting information being displayed at stations.
A map of this sort can be condensed into a fold-out pocket size (again as London and other cities manage very effectively) and can be poster-sized with maximum visual impact just as readily.
No map will capture every little nuance of the service pattern while still being effective and easy to read. The Altona loop and Williamstown services could be different colours but are fundamentally a part of the same service group even if they don't enjoy through trains between each and every station at all times. Alamein is shown suitably as part-time through to the City so perhaps Williamstown could be likewise in its own colour. Too many colours together tends to confuse and detract from the overall impact however.
It gets a thumbs-up from me.