It is difficult to say why something did not happen however the comparison with the USA's river systems is apt. Cities are more likely to grow in locations where there is a transport node or interchange. That is, where travelling goods and people are forced to change from one form of long distance transport to another. This can allow for the development of trade entrepots and industries reliant on both local and imported goods. For example, you are likely to get cities forming as ports in suitable river estuaries where bulk seagoing cargo can be loaded or unloaded for transport to or from the hinterland by road, rail, or riverboat. On navigable river systems you are likely to have cities form as river ports either where they form a connection with other forms of transport, particularly at river crossings, or at the upper points of navigability.

In Australia the state capitals are all situated on sea ports at the mouth of a river. The Murray Darling river system is not one of those rivers despite being the longest in Australia.

The reason this is an issue for the Murray Darling river system is that it is not dependably navigable. The mouth of the Murray at Murray Mouth in South Australia is a shallow estuary which regularly silts up and is not suitable for seagoing ships. The Murray was quite heavily trafficked by flat bottomed paddle wheelers up as far as Echuca although the travel depended on the season and water levels being high enough. Beyond Echuca smaller boats could get up as far as Albury/Wodonga reasonably reliably. Agricultural produce, particularly the annual wool clip, which wasn't perishable, could be shipped down from the Riverina when the Murray and it's tributaries were high. The train line crossing Victoria from Melbourne connected to Echuca so Echuca did become a major river port as a transport interchange for goods shipped on the Murray, however as more train lines and road networks were developed the importance of the less reliable river transport was reduced. Echuca still has a port but it is mainly for tourists.

Albury (NSW) and Wodonga (VIC) sit on opposite sides of the Murray and are connected by a bridge. Together they form a significantly sized pair of cities. They sit on the major highway connecting Sydney and Melbourne (the largest two cities in Australia) and until 1962 also formed the interchange point for the New South Wales standard gauge and the Victorian broad gauge train line so passengers and freight travelling North or South all had to disembark there and change trains.

The Darling, coming down from much further north also allowed seasonal shipping of agricultural products down to towns that had railroad connections but this limited freight movement did not provide support for industry or development of cities.

So the major difference is the limited navigability and that the bulk goods which were transported were largely limited to agricultural produce.