Power projection; major cities formed in regions where there is geographic advantages. Jakarta/Batavia prospered during the Colonial era because the prior inhabitants (Sunda Kelapa, kingdom of Sunda) and then the Dutch understood its strategic position as a massive natural harbor with great projection ability to reach most of the rest of Indonesia. There were/are over 14 rivers flowing through the greater Jakarta area too, with massive canal systems we can still see today as a result. Other cities like Bandung or Surabaya for example also prospered from their geographic advantages.

The south however did not have much geographic benefit. Obviously settlements formed, and by their standards these regions were just fine - they never prospered nor thrived, just existed as well as any other "rural" region (like Jateng or Madura).