East Timor goes even worse than in OTL. Australia ultimately attacks the Indonesians with American assistance in order to stop the massacres. The resulting destruction of the Indonesian military encourages every independence movement to take advantage of the power vacuum and secede. Give it 10 to 15 years, assuming that no outside intervenes to put it back together, and Indonesia is reduced to Java, some of the islands to the east of it, and maybe southern Sumatra.