It is the ridiculous idea of having one zone for all of Melbourne that makes a short trip uneconomic whilst encouraging people to live way out on the fringes.
As is just about always the case, Singapore leads the way.
Their Ez Link card system works on a "flagfall plus as the crow flies" fare system. You are charged from where your journey starts to where it ends. Any excess mileage as you change modes of tranport to get to your destination is recalculated on your last touch off to deduct the correct fare. It is the system we should have. Unfortunately, we had to dumb down our fare system so that Myki could cope.