Like our electricity network, I think we've spent excessively on gold playing rather than new lines or the stuff that matters. Melbourne runs well on a basic system.
Have track foot crossings 'at grade' rather than using overpasses and tunnels
Waive the "no level crossing" rule for any new suburban line
Use unfenced corridors for new suburban lines
Use a video screen system to reduce use of guards or "flag savers".
In high demand spots, make station carpark users use their ticket to exit or pay parking fees - with opal a new arrangement will have to be found later however
One fare/ticket to cover all modes rather than paying extra to change service
Remove some seats from some rail cars.
I agree there is a form of "gold-plating" in some areas of the railway, but perhaps not the ones you are thinking of.
Importantly, perceptions of gold-plating are subject to political vicissitudes, economic conditions, comparisons, personal and corporate agendas, technological trends, ulterior motives and so on. We often hear of gold-plating when it is time to renew infrastructure and there are plans to somehow downgrade. What one man considers gold-plating might be seen by another as essential. Many risks protected against with what some might see as "gold-plated engineering controls" were originally unmanaged; sometimes those controls are reviewed and removed - they have a way of gradually being melted down by market forces and shifts in politics, for better or worse - I'd say usually for the worse. Watch that space.
Also, I feel that some of the things you have listed are not necessarily gold-plating or excessive redundancy, but justified for safety reasons while in some cases also appearing as remnants of the past. Remnants of the past that could be subject to removal in the future include Guards, station staff giving rightaway handsignals, etc., but whether they are really redundant is not always something that can be determined absolutely. Sure, the technology exists to do away with them, Drivers, Signallers and so on, but that does not mean it is a great idea to implement it, politically acceptable, affordable, etc. Perceptions and the goal posts of safety are subject to move in either direction, so watch that space, too. That's politics.
There is a lot of gold-plating in NSW railways in terms of personnel, namely the extensive bureaucratic empires comprised largely of people with impressive job titles, position descriptions and gold-plated salaries, but who do little to actually move trains, let alone move them better. Apparently some of this has been trimmed of late, but a lot has definitely survived, been moved, renamed, split up etc. the net result being it's still there. As we move towards more private sector involvement, don't assume that will solve the bureaucratic issues, either. Private companies on the take from the State do not always have the incentive to do right by its citizens, and can become inefficient, if not corrupt rent-seekers that are even worse than State-owned entities. Think it will be set up so that can't happen? Believe it when you see it. Oh, and the State regulatory, planning, infrastructure owning and operational bureaucracies would probably still be there, hidden away from the public eye.
Transverse seating is the way it has always been done (except in the ends of suburban cars etc.), but a longitudinal seating trial of sorts is underway.
Sydney once had far more level crossings than it does now, including in what are now some very busy locations like Croydon and Burwood (removed from both locations in 1892). If road traffic decreased due to some sort of major change in society (e.g. economic collapse) or somehow a culture of individual responsibility and respect for State property was reborn, standards of living and the value of human life fell, etc., maybe level crossings or open corridors wouldn't be seen as such a liability, at least outside busy multiple line areas. Of course, open corridors and level crossings could be a good reason to keep front line staff rather than indulge in sexy technology, as could an economic slowdown.