More zones? You only have to look at the neighbourhood system to see why they got rid of that idea 30+ years ago.
Naturally, if they did make more zones, the boundaries would be "strategically" placed one station short of a major interchange or location too. Lilydale-Ringwood East, Ringwood-Nunawading, Blackburn-Mont Albert, Surrey Hills-East Camberwell, Camberwell-Hawthorn... yeah, it sounds ridiculous already and that's only one line done. The Belgrave line just happens to fit too, as it is a multiple of four: Belgrave-Upper Ferntree Gully and Ferntree Gully-Heathmont.
As the zones are so close together, there is no way to implement an overlap either - the poor bast who wants to go from Ferntree Gully to Upper F/G, or anyone who has to change trains at the three interchange stations (Ringwood, Camberwell, Burnley) now has to pay for an extra zone despite going straight back to the previous zone (and all three stations, depending on the platform, require you to exit the paid area; Ringwood and Camberwell also have barriers on platforms 1+2, forcing a touch-off if you have to use platform 3).
I have a better idea, close practically every second station between Ringwood to Richmond and I might pay extra for a much quicker ride...
Heatherdale. Both were a complete waste of money rebuilding them, they should have levelled them and sped up the line (no doubt, when they sink the tracks, Heatherdale will magically cost billions of dollars for the 20-something people that use it per day, and take five minutes to figure out where the platforms are just like Mitcham - methinks the exit will be at the Eastlink end nowhere near Heatherdale Rd, just to spite passengers (pro-car movement, politicians stuck in the 1950s, etc.), knowing full well that the frequency of the 742 is nothing short of pathetic and will probably leave while everyone is walking back to the main road).
Laburnum doesn't even deserve a mention. Where's that centre express track anyway? The signals for the centre track have been there for a number of years now.
Mont Albert can be converted into an expensive cafe or something for the cashed-up NIMBYs. Double the 766 frequency, see if anyone catches it; if not, back to the old frequency (Mont Albert is the home to six-figure-dollar cars after all, second only to Toorak). Canterbury Rd is where the buses are really needed; the 765 and 679 are the only two of mention, however both are only average services (the 285 is a myth, no-one even saw it, let alone caught it), nothing of SmartBus quality.
Chatham's main building can be relocated and made into something useful/"fun" just like the Ringwood signal box was.
East Camberwell has had no historical significance whatsoever since 1986 (the tiny building on platform 3 hardly counts; put it in the park near Camberwell or on the Outer Circle trail if it must be preserved).
Auburn is probably the only "even" station on the line since Nunawading to get more than a handful of people, yet it's also unstaffed (as with Canterbury - I don't count "host" stations as staffed). I believe there's a model railway club somewhere around there, but I haven't looked... It's also a ten minute walk from Glenferrie (15 minutes from Camberwell if you follow Burwood Rd to the railway cutting, unless there's a quicker way I don't know).
Hawthorn. Historical wooden building with historical wooden steps between platforms and part of the roof from the 1800s Flinders Street, and home to AOs and PSOs rather than actual station staff. Not moving any time soon.
Trains already pass through there more often than not, so I don't need to mention East Richmond beyond saying that Coles is no longer there (it moved inside Dimmeys).