The chief Problem is that the ocean between Indonesia and Australia being infamously hard to cross without relatively modern (post 19th Century) ships that could either run on their own power, OR capable to run with the softest of wind. They were intermittent very rough sea between days of dead wind, something that is nightmare for ships who rely on wind for their main mobility.
If the seas were much more stable there, you'll bet there would be Javanese or Makassar Kingdom there.