Due to the nature of the question it's difficult to answer, as we are not only dealing with a hypothetical (as the mods noted) but also a vast stretch of time. There are a couple of factors I can think of off the top of my head.

Geography would be a major factor. Sure, the east coast of Australia is verdant (especially in the northeast), but the areas nearest Indonesia go from mangroves to desert pretty quickly. On the west coast it isn't until you go a long way south that you enter the 'Mediterranean' climate zone where Perth is. As you can see from the map, even the bulk of Indonesia is a long way from the top of Western Australia.

Another aspect is one of trade. With a low population density, and limited production of trade goods, there would have been very little incentive to move to/colonise Australia. Indonesia/Malaysia occupies a fantastic position geographically for trade, especially in the China --> India --> Middle East trade routes which were the central routes of world trade for much of history.

A third (and final) consideration would be the focus of Indonesian polities: culturally and religiously Indonesia was very strongly focused toward South and Southeast Asia. This is what I've heard referred to as the "Hindusphere" - Indian religious, philosophical, and political concepts dominated Southeast Asia and the archipelago for a long time.

Later European explorers were initially also focused on their region. The first waves of Eastern exploration were primarily focused on interrupting Muslim (and Venetian) control of the China -> India -> Middle East route (from the ME to Venice, and then into the rest of Europe) for economic gain by those European polities (and weaken their rivals). Later colonialising efforts in Asia were also financially-motivated (first Portugal then Britain in the Indian subcontinent, the French in SE Asia, Spain then the Dutch in Indonesia), but were also motivated by Imperialist concepts. Australia, unlike the colonizing of India, for example, was a "colony of settlement", rather than a "colony of conquest". Both serve primarily as means for maximum extraction of resources, but in Australia those resources would need to be developed and exploited directly by the Europeans, rather than taken from existing markets and local polities.

Hey there,

Just to let you know, your question is fine, and we're letting it stand. However, you should be aware that questions framed as 'Why didn't X do Y' relatively often don't get an answer that meets our standards (in our experience as moderators). There are a few reasons for this. Firstly, it often can be difficult to prove the counterfactual: historians know much more about what happened than what might have happened. Secondly, 'why didn't X do Y' questions are sometimes phrased in an ahistorical way. It's worth remembering that people in the past couldn't see into the future, and they generally didn't have all the information we now have about their situations; things that look obvious now didn't necessarily look that way at the time.

If you end up not getting a response after a day or two, consider asking a new question focusing instead on why what happened did happen (rather than why what didn't happen didn't happen) - this kind of question is more likely to get a response in our experience. Hope this helps!