Over the last decade in particular, there have been challenges to the orthodox archaeological and linguistic model of Neolithic expansion out of Taiwan, through the Philippines and Eastern Indonesia / Wallacea and out into the Pacific. There have been suggestions that Taiwan was not the origin but merely a backwater with the Neolithic developing independently within the Philippines-Indonesia and perhaps spreading back to Taiwan, or that its origin point was southern China or Vietnam direct to the Philippines. Strong agricultural influences from the New Guinea centre of agricultural development have also been claimed. Another suggestion is for two “Neolithics”, with one spreading down the Malay Peninsula and into Sumatra and parts of Java and Borneo at about the same time, or even before a Taiwan-derived spread. The paper discusses which of these many confusing suggestions have merit and whether it is possible to synthesize the picture emerging from the many new studies in the region into a general explanatory framework.