The only thing close is that Edenhope, Cobden, and Corryong don't have Vline services, which is true (they have extended town bus services).
With regards to the Ararat train, I suspected all along what you were really saying is that people should spend longer on a train and less time on a bus (which is fair enough) but I feel the current arrangement actually works better because there's a larger catchment of potential passengers along the Glenelg and almost none along the Pyrenees. Fair enough to utilise the train better but the catchment is much larger along the Glenelg.
There's a much larger catchment on the Ararat line - the more passengers you get on that train, the greater the potential for added services, which cycles into more patronage.
If you gave Hamilton passengers the choice between an hour extra on the train (but 15 minutes longer overall) and the current arrangement I have no doubt that a shorter transit time would win hands down.
I don't think it would even be that much longer - even with a 10 minute change, it would be 1hr45min to Glenthompson, which is about the same as the coach from Ballarat (and that's with the long train dwell time at Ballarat).
We've also seen from the likes of the Mildura Train Action Group how much people apparently hate buses compared with trains, regardless of journey time.