two cities are enough in Java, particularly a Sundanese city (Sundapura - then Jakarta, or Pajajaran or Bandung, etc) and a Javanese city (Trowulan, or Surabaya, or Singhasari - then Malang, etc). That setting, or a single city in the middle (Mataram - then Jogjakarta or Daha - then Kediri, etc) allowing more space for Palembang in Sumatra and Denpasar of Bali in the easternmost amalgamated island.
Comparing with the size of Borneo and other islands, I prefer Java to be a single row island though.