From my experience, the bike storage on V/Line's Vlocity trains is quite adequate. Vertical bike storage would take up more dedicated space, whereas the current arrangement can also be used to carry wheel-on luggage and so on. It's certainly a step-up from the arrangement on the N-sets, which is to throw the bike in the power/luggage van.
Vertical bike storage actually takes up less floor space than horizontal bike storage.
Suburban trains don't need dedicated spaces, they tend to have more open space around the doors (to cram more commuters into them during peak periods) than regional/'country' trains. Sure, you might have to stand up to hold on to your bike but the shorter trip duration offsets that.
In order to avoid the stuggles of taking a bike on a train, there needs to be a way of safely securing your bike, and this may require bicycle spaces. Here in Melbourne, a lot of suburban stations are within walking
distance of each other so it's often easier just to walk to and from stations that, well, standing up and holding onto a bike on the train. This is not to say bikes should not be permitted.
Unfortunately, we don't run that many express services here in Melbourne, I wish we could do so. These often go for long enough without stopping that bicycle commuters would be a bigger consideration.
Now bike parking at stations... that's another matter. Perth and Brisbane have the right idea in having bike shelters that use their respective transit smartcards for access control - it should be just as easy as taking the bus to the station. It's a pity that we're not likely to see any car parking spaces removed at any Australian railway station to put in secure bike parking (3 car spaces can fit a 50 bike cage). It's a lot quicker to just install them in car parks.
We have some secure bike parking here but it can't be accessed with our myki cards.